Process merged multiome objects

Libraries

library(tidyr)
library(dplyr)
library(ggplot2)
library(purrr)
library(readr)
library(viridis)
library(Seurat)
library(Signac)
library(Azimuth)
library(EnsDb.Hsapiens.v86)
library(BSgenome.Hsapiens.UCSC.hg38)
library(GenomicRanges)
library(harmony)
library(data.table)

set.seed(1234)
options(repr.matrix.max.cols=100, repr.matrix.max.rows=50)
options(warn=-1)

source("../../../functions_r/scRNAseq.R")

ggplot2::theme_set(theme_min())

Set up object

brain_region <- 'DLPFC'
data_dir = '/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/03-integration/merged_objects/'
integrated_object_path = paste0(data_dir, brain_region, '.merged.multiome.rds')
metadata_all_path = '/oak/stanford/groups/akundaje/projects/psychencode/outs/7_26_2023_multiome_analysis/metadata/multiome.qc.tsv'

integrated_object_path

## [1] "/oak/stanford/groups/akundaje/projects/psychencode/outs/20231009_multiome_analysis/03-integration/merged_objects/DLPFC.merged.multiome.rds"

obj <- readRDS(integrated_object_path)
obj

## An object of class Seurat 
## 384045 features across 155745 samples within 2 assays 
## Active assay: RNA (36601 features, 0 variable features)
##  2 layers present: counts, data
##  1 other assay present: ATAC

Version(obj)

## [1] '5.0.0'

# add 'sample' column
obj@meta.data$sample <- obj@meta.data$orig.ident
head(obj@meta.data)

##                                                           orig.ident nCount_RNA
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 1041-Schizophrenia-DLPFC     108417
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 1041-Schizophrenia-DLPFC     107724
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 1041-Schizophrenia-DLPFC     107524
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 1041-Schizophrenia-DLPFC     106935
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 1041-Schizophrenia-DLPFC     105048
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 1041-Schizophrenia-DLPFC     104851
##                                             nFeature_RNA            barcode
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1        10308 GCTGAGGAGTATTGCA-1
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1         9747 ACACTTGCAATAGCCC-1
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1         9608 ATAGCATGTCCTTCTC-1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1        10107 TCTAACCGTTTCCACG-1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1         9579 CATAGTCAGCGCATTG-1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1         9755 AGTAATCGTTGAGGTC-1
##                                                    gex_barcode
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 GCTGAGGAGTATTGCA-1
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 ACACTTGCAATAGCCC-1
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 ATAGCATGTCCTTCTC-1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 TCTAACCGTTTCCACG-1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 CATAGTCAGCGCATTG-1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 AGTAATCGTTGAGGTC-1
##                                                   atac_barcode is_cell
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 CATTCCTTCCAGCTCG-1       1
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 TAGTGAGGTTGAAGCA-1       1
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 CGGTGCACAATTAGCG-1       1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 AGGGATGCAGGCCAAT-1       1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 TTGTCCTTCAAACCGG-1       1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 TCACTCGCAAACTAAC-1       1
##                                             excluded_reason gex_raw_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1               0        279080
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1               0        269689
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1               0        275695
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1               0        282987
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1               0        282530
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1               0        268611
##                                             gex_mapped_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1           267535
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1           259264
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1           264532
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           272074
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1           270917
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1           258173
##                                             gex_conf_intergenic_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                     23071
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                     19774
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                     22510
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                     20599
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                     19743
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                     17299
##                                             gex_conf_exonic_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 32996
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 30581
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 31128
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 38103
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 35107
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 32733
##                                             gex_conf_intronic_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                  198681
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                  197344
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                  198642
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                  201737
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                  203135
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                  197170
##                                             gex_conf_exonic_unique_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                        30045
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                        27987
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                        28331
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                        34999
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                        31112
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                        29883
##                                             gex_conf_exonic_antisense_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            2756
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            2429
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            2632
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            2928
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            3836
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            2689
##                                             gex_conf_exonic_dup_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                     14008
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                     13100
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                     13107
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                     17221
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                     14928
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                     14159
##                                             gex_exonic_umis
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1           15499
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1           14444
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1           14770
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           17250
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1           15681
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1           15234
##                                             gex_conf_intronic_unique_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                         182796
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                         184001
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                         182381
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                         184894
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                         179669
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                         181608
##                                             gex_conf_intronic_antisense_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             12717
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                              9894
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             12417
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             13502
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             19490
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             12504
##                                             gex_conf_intronic_dup_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                       86797
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                       87866
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                       86812
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                       92257
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                       87472
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                       89096
##                                             gex_intronic_umis
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1             92977
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1             93355
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1             92827
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1             89760
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1             89425
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1             89682
##                                             gex_conf_txomic_unique_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                        28386
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                        26528
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                        26683
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                        33132
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                        29310
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                        28332
##                                             gex_umis_count gex_genes_count
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1         108476           10313
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1         107799            9759
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1         107597            9615
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1         107010           10114
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1         105106            9586
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1         104916            9769
##                                             atac_raw_reads atac_unmapped_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1          37251                 317
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          67566                 541
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1          34744                 277
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           1965                  15
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1          27341                 245
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1          58127                 453
##                                             atac_lowmapq atac_dup_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1         2412           6829
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1         4574          12611
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1         2198           6472
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1          116            398
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1         1787           5066
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1         4717          11178
##                                             atac_chimeric_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                  32
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                  50
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                  35
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                   1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                  46
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                  58
##                                             atac_mitochondrial_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                       41
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                      442
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                       23
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                        3
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                        8
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                      218
##                                             atac_fragments atac_TSS_fragments
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1          27612               5204
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          49325               7609
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1          25734               5238
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           1431                362
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1          20181               4141
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1          41475               6426
##                                             atac_peak_region_fragments
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                       5880
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                       8465
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                       5479
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                        426
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                       4772
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                       6819
##                                             atac_peak_region_cutsites
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                     10519
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                     15216
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                      9984
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                       787
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                      8694
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                     12143
##                                             nCount_ATAC nFeature_ATAC
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1       13030         11777
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1       19875         17268
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       11366         10124
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1         774           761
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1        9755          8826
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1       16264         14366
##                                             nucleosome_signal
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1         1.3715430
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1         1.2471058
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1         1.1082791
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1         1.2800000
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1         1.2413956
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1         0.9808066
##                                             nucleosome_percentile
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                  0.93
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                  0.89
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                  0.83
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                  0.90
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                  0.89
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                  0.75
##                                             TSS.enrichment TSS.percentile
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1       2.450345           0.32
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1       2.191072           0.30
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       3.002553           0.41
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1       4.595405           0.68
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1       2.999511           0.41
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1       2.338303           0.31
##                                             pct_frags_in_peaks percent.mt
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1           21.29509 0.08116808
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1           17.16168 0.10489770
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1           21.29090 0.15531416
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           29.76939 0.15523449
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1           23.64600 0.05426091
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1           16.44123 0.14592136
##                                             nCount_SCT nFeature_SCT
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1       5966         2478
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1       6007         2216
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       6318         2354
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1       5989         2588
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1       6128         2426
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1       6027         2297
##                                             nCount_refAssay nFeature_refAssay
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1          108417             10308
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          107724              9747
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1          107524              9608
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1          106935             10107
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1          105048              9579
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1          104851              9755
##                                             predicted.class.score
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                     1
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                     1
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                     1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                     1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                     1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                     1
##                                             predicted.class
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1   Glutamatergic
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1   Glutamatergic
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       GABAergic
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1   Glutamatergic
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1   Glutamatergic
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1   Glutamatergic
##                                             predicted.cluster.score
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1               0.5883295
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1               0.5740826
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1               0.4487918
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1               0.5479081
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1               1.0000000
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1               0.6140496
##                                                       predicted.cluster
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1      Exc L2 LINC00507 GLRA3
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          Exc L3-5 RORB LNX2
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       Inh L5-6 PVALB KCNIP2
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1     Exc L6 THEMIS LINC00343
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 Exc L5-6 FEZF2 C9orf135-AS1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1      Exc L5 THEMIS SLC22A18
##                                             predicted.subclass.score
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                0.8557476
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                1.0000000
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                0.9240861
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                0.9498290
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                1.0000000
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                1.0000000
##                                             predicted.subclass
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1            L2/3 IT
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1              L5 IT
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1              Pvalb
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1              L6 IT
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1              L6 CT
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1              L5 IT
##                                             predicted.cross_species_cluster.score
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             0.8240176
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             0.9845528
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             0.7955298
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             0.5529920
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             1.0000000
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             0.9873519
##                                             predicted.cross_species_cluster
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                         L2/3 IT
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                         L5 IT_2
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                         Pvalb_1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                         L6 IT_1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                         L6 CT_2
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                         L5 IT_2
##                                             mapping.score SCT_snn_res.0.8
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1     0.9784835               7
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1     1.0000000              11
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1     1.0000000              15
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1     0.7423896               6
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1     0.9711277              13
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1     0.9881113              11
##                                             seurat_clusters atac_doublets
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1               7       singlet
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1              11       singlet
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1              15       singlet
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1               6       singlet
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1              13       singlet
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1              11       singlet
##                                             pANN_0.25_0.01_374
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1          0.2696629
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          0.1797753
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1          0.1348315
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1          0.1123596
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1          0.1123596
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1          0.2808989
##                                             DF.classifications_0.25_0.01_374
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                          Singlet
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                          Singlet
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                          Singlet
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                          Singlet
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                          Singlet
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                          Singlet
##                                             rna_doublets all_doublets region
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1      singlet      singlet  DLPFC
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1      singlet      singlet  DLPFC
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1      singlet      singlet  DLPFC
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1      singlet      singlet  DLPFC
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1      singlet      singlet  DLPFC
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1      singlet      singlet  DLPFC
##                                             pANN_0.25_0.01_198
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_198
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_409
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_409
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_6
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1               NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1               NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1               NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1               NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1               NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1               NA
##                                             DF.classifications_0.25_0.01_6
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                           <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                           <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                           <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                           <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                           <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                           <NA>
##                                             pANN_0.25_0.01_76
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_76
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_280
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_280
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_141
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_141
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_287
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_287
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_188
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_188
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_77
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_77
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_196
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_196
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_203
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_203
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_73
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_73
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_370
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_370
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_127
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_127
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_269
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_269
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_37
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_37
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_403
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_403
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_144
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_144
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_500
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_500
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_503
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_503
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_140
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_140
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_60
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_60
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_83
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_83
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_64
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_64
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_134
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_134
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_75
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_75
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_193
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_193
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_182
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_182
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_120
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_120
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_186
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_186
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_183
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_183
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_115
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_115
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_71
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_71
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                                               sample
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 1041-Schizophrenia-DLPFC

dim(obj@meta.data)

## [1] 155745    130

# get patient metadata
metadata_samples_all <- read.csv(metadata_all_path, sep='\t')
head(metadata_samples_all)

##                     sample subject_id     diagnosis brain_region    sex  age
## 1        1317-Bipolar-dACC       1317       Bipolar         dACC Female 56.6
## 2 1320-Schizophrenia-DLPFC       1320 Schizophrenia        DLPFC   Male 53.2
## 3        1390-Control-dACC       1390       Control         dACC Female 42.7
## 4        1713-Bipolar-dACC       1713       Bipolar         dACC   Male 20.7
## 5       1317-Bipolar-DLPFC       1317       Bipolar        DLPFC Female 56.6
## 6       1390-Control-DLPFC       1390       Control        DLPFC Female 42.7
##                        race              ethnicity pulsar_id pmi_hours
## 1                     White Not Hispanic or Latino     13957     26.50
## 2 Black or African-American Not Hispanic or Latino     13959     40.50
## 3 Black or African-American Not Hispanic or Latino     13963      8.17
## 4                     White Not Hispanic or Latino     13996     26.50
## 5                     White Not Hispanic or Latino     13956     26.50
## 6 Black or African-American Not Hispanic or Latino     13961      8.17
##   tissue_pH         RIN                  original_name  swap batch    SREQ
## 1      5.81         2.1              1317-Bipolar-dACC False     1 436/437
## 2      6.52         8.9       1320-Schizophrenia-DLPFC False     1 436/437
## 3      6.34         8.9              1390-Control-dACC False     1 436/437
## 4      6.45           7              1713-Bipolar-dACC False     1 436/437
## 5      5.81 N/A too low             1317-Bipolar-DLPFC False     2 439/440
## 6      6.34         7.7 1320-Schizophrenia-Hippocampus  True     2 439/440
##   who.nuclei_prep who.multiome       date     qc_rna qc_atac num_cells
## 1          Yiling         Joan 10/13/2021       fail    pass      7885
## 2          Yiling         Joan 10/13/2021       pass    pass      4763
## 3          Yiling         Joan 10/13/2021       pass    pass      2854
## 4          Yiling         Joan 10/13/2021 borderline    pass      7212
## 5          Yiling        Minyi 10/22/2021       fail    fail      5337
## 6          Yiling        Minyi 10/22/2021       pass    pass      7128
##   mean_rna_reads mean_atac_reads median_high_quality_fragments tss_enrichment
## 1       25741.51        25952.11                        5696.0         5.9193
## 2       40303.93        29276.88                        8747.0         6.7518
## 3       65877.85        68351.57                       11856.5         5.6492
## 4       28831.78        25978.22                        4010.5         7.7729
## 5       21499.03        19824.73                        4951.0         3.8609
## 6       12446.31        14240.00                        4974.5         6.1892
##   median_genes median_umi   q30_rna  q30_atac   q30_all
## 1          112      160.0 0.9518203 0.9372318 0.9446584
## 2         1369     2452.0 0.9481870 0.9137288 0.9340603
## 3         2378     6267.5 0.9471261 0.9336242 0.9404008
## 4          244      274.0 0.9473116 0.9324500 0.9404322
## 5          463      766.0 0.9546507 0.9320030 0.9440367
## 6         1471     2821.0 0.9515652 0.9348879 0.9428508
##                                                                                                                 oak_path
## 1              /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC
## 2       /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC
## 3              /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC
## 4              /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC
## 5             /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus
##                                                                                                                                                                        outs_path
## 1                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs
## 2             /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs
## 3                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs
## 4                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs
## 5                         /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs
##                                                                                                                                                                                  metrics_csv
## 1                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/summary.csv
## 2             /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/summary.csv
## 3                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/summary.csv
## 4                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/summary.csv
## 5                         /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/summary.csv
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/summary.csv
##                                                                                                                                                                                            raw_rna_counts
## 1                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/raw_feature_bc_matrix.h5
## 2             /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/raw_feature_bc_matrix.h5
## 3                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/raw_feature_bc_matrix.h5
## 4                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/raw_feature_bc_matrix.h5
## 5                         /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/raw_feature_bc_matrix.h5
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/raw_feature_bc_matrix.h5
##                                                                                                                                                                                            filtered_rna_counts
## 1                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/filtered_feature_bc_matrix.h5
## 2             /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/filtered_feature_bc_matrix.h5
## 3                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/filtered_feature_bc_matrix.h5
## 4                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/filtered_feature_bc_matrix.h5
## 5                         /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/filtered_feature_bc_matrix.h5
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/filtered_feature_bc_matrix.h5
##                                                                                                                                                                                         atac_fragments
## 1                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/atac_fragments.tsv.gz
## 2             /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/atac_fragments.tsv.gz
## 3                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/atac_fragments.tsv.gz
## 4                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/atac_fragments.tsv.gz
## 5                         /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/atac_fragments.tsv.gz
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/atac_fragments.tsv.gz
##                                                                                                                                                                                      per_barcode_metrics
## 1                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/per_barcode_metrics.csv
## 2             /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/per_barcode_metrics.csv
## 3                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/per_barcode_metrics.csv
## 4                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/per_barcode_metrics.csv
## 5                         /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/per_barcode_metrics.csv
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/per_barcode_metrics.csv
##                                                                                                                                                                                     gex_molecule_info
## 1                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1317-Bipolar-dACC/SREQ-436-437-3_1317-Bipolar-dACC_outs/outs/gex_molecule_info.h5
## 2             /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1320-Schizophrenia-DLPFC/SREQ-436-437-4_1320-Schizophrenia-DLPFC_outs/outs/gex_molecule_info.h5
## 3                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1390-Control-dACC/SREQ-436-437-5_1390-Control-dACC_outs/outs/gex_molecule_info.h5
## 4                           /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-436_437/1713-Bipolar-dACC/SREQ-436-437-6_1713-Bipolar-dACC_outs/outs/gex_molecule_info.h5
## 5                         /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1317-Bipolar-DLPFC/SREQ-439-440-1_1317-Bipolar-DLPFC_outs/outs/gex_molecule_info.h5
## 6 /oak/stanford/groups/akundaje/projects/psychencode/data/psychENCODE_shared/SREQ-439_440/1320-Schizophrenia-Hippocampus/SREQ-439-440-3_1320-Schizophrenia-Hippocampus_outs/outs/gex_molecule_info.h5

dim(metadata_samples_all)

## [1] 111  39

# add patient metadata to cell metadata
cell_meta <- obj@meta.data
cell_meta <- left_join(cell_meta, metadata_samples_all %>% 
                         dplyr::select(sample, condition = diagnosis, 
                                       region = brain_region, donor = subject_id, 
                                       batch, sex, age, race, 
                                       source = who.multiome), by = 'sample')
rownames(cell_meta) <- rownames(obj@meta.data)
# put our new metadata back
obj@meta.data <- cell_meta
head(obj@meta.data)

##                                                           orig.ident nCount_RNA
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 1041-Schizophrenia-DLPFC     108417
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 1041-Schizophrenia-DLPFC     107724
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 1041-Schizophrenia-DLPFC     107524
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 1041-Schizophrenia-DLPFC     106935
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 1041-Schizophrenia-DLPFC     105048
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 1041-Schizophrenia-DLPFC     104851
##                                             nFeature_RNA            barcode
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1        10308 GCTGAGGAGTATTGCA-1
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1         9747 ACACTTGCAATAGCCC-1
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1         9608 ATAGCATGTCCTTCTC-1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1        10107 TCTAACCGTTTCCACG-1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1         9579 CATAGTCAGCGCATTG-1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1         9755 AGTAATCGTTGAGGTC-1
##                                                    gex_barcode
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 GCTGAGGAGTATTGCA-1
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 ACACTTGCAATAGCCC-1
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 ATAGCATGTCCTTCTC-1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 TCTAACCGTTTCCACG-1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 CATAGTCAGCGCATTG-1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 AGTAATCGTTGAGGTC-1
##                                                   atac_barcode is_cell
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 CATTCCTTCCAGCTCG-1       1
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 TAGTGAGGTTGAAGCA-1       1
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 CGGTGCACAATTAGCG-1       1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 AGGGATGCAGGCCAAT-1       1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 TTGTCCTTCAAACCGG-1       1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 TCACTCGCAAACTAAC-1       1
##                                             excluded_reason gex_raw_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1               0        279080
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1               0        269689
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1               0        275695
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1               0        282987
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1               0        282530
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1               0        268611
##                                             gex_mapped_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1           267535
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1           259264
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1           264532
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           272074
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1           270917
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1           258173
##                                             gex_conf_intergenic_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                     23071
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                     19774
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                     22510
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                     20599
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                     19743
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                     17299
##                                             gex_conf_exonic_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 32996
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 30581
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 31128
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 38103
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 35107
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 32733
##                                             gex_conf_intronic_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                  198681
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                  197344
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                  198642
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                  201737
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                  203135
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                  197170
##                                             gex_conf_exonic_unique_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                        30045
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                        27987
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                        28331
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                        34999
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                        31112
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                        29883
##                                             gex_conf_exonic_antisense_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            2756
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            2429
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            2632
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            2928
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            3836
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            2689
##                                             gex_conf_exonic_dup_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                     14008
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                     13100
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                     13107
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                     17221
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                     14928
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                     14159
##                                             gex_exonic_umis
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1           15499
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1           14444
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1           14770
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           17250
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1           15681
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1           15234
##                                             gex_conf_intronic_unique_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                         182796
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                         184001
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                         182381
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                         184894
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                         179669
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                         181608
##                                             gex_conf_intronic_antisense_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             12717
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                              9894
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             12417
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             13502
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             19490
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             12504
##                                             gex_conf_intronic_dup_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                       86797
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                       87866
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                       86812
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                       92257
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                       87472
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                       89096
##                                             gex_intronic_umis
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1             92977
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1             93355
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1             92827
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1             89760
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1             89425
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1             89682
##                                             gex_conf_txomic_unique_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                        28386
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                        26528
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                        26683
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                        33132
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                        29310
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                        28332
##                                             gex_umis_count gex_genes_count
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1         108476           10313
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1         107799            9759
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1         107597            9615
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1         107010           10114
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1         105106            9586
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1         104916            9769
##                                             atac_raw_reads atac_unmapped_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1          37251                 317
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          67566                 541
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1          34744                 277
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           1965                  15
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1          27341                 245
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1          58127                 453
##                                             atac_lowmapq atac_dup_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1         2412           6829
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1         4574          12611
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1         2198           6472
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1          116            398
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1         1787           5066
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1         4717          11178
##                                             atac_chimeric_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                  32
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                  50
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                  35
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                   1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                  46
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                  58
##                                             atac_mitochondrial_reads
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                       41
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                      442
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                       23
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                        3
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                        8
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                      218
##                                             atac_fragments atac_TSS_fragments
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1          27612               5204
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          49325               7609
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1          25734               5238
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           1431                362
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1          20181               4141
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1          41475               6426
##                                             atac_peak_region_fragments
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                       5880
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                       8465
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                       5479
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                        426
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                       4772
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                       6819
##                                             atac_peak_region_cutsites
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                     10519
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                     15216
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                      9984
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                       787
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                      8694
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                     12143
##                                             nCount_ATAC nFeature_ATAC
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1       13030         11777
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1       19875         17268
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       11366         10124
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1         774           761
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1        9755          8826
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1       16264         14366
##                                             nucleosome_signal
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1         1.3715430
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1         1.2471058
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1         1.1082791
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1         1.2800000
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1         1.2413956
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1         0.9808066
##                                             nucleosome_percentile
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                  0.93
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                  0.89
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                  0.83
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                  0.90
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                  0.89
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                  0.75
##                                             TSS.enrichment TSS.percentile
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1       2.450345           0.32
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1       2.191072           0.30
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       3.002553           0.41
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1       4.595405           0.68
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1       2.999511           0.41
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1       2.338303           0.31
##                                             pct_frags_in_peaks percent.mt
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1           21.29509 0.08116808
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1           17.16168 0.10489770
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1           21.29090 0.15531416
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1           29.76939 0.15523449
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1           23.64600 0.05426091
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1           16.44123 0.14592136
##                                             nCount_SCT nFeature_SCT
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1       5966         2478
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1       6007         2216
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       6318         2354
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1       5989         2588
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1       6128         2426
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1       6027         2297
##                                             nCount_refAssay nFeature_refAssay
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1          108417             10308
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          107724              9747
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1          107524              9608
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1          106935             10107
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1          105048              9579
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1          104851              9755
##                                             predicted.class.score
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                     1
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                     1
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                     1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                     1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                     1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                     1
##                                             predicted.class
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1   Glutamatergic
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1   Glutamatergic
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       GABAergic
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1   Glutamatergic
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1   Glutamatergic
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1   Glutamatergic
##                                             predicted.cluster.score
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1               0.5883295
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1               0.5740826
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1               0.4487918
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1               0.5479081
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1               1.0000000
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1               0.6140496
##                                                       predicted.cluster
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1      Exc L2 LINC00507 GLRA3
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          Exc L3-5 RORB LNX2
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1       Inh L5-6 PVALB KCNIP2
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1     Exc L6 THEMIS LINC00343
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 Exc L5-6 FEZF2 C9orf135-AS1
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1      Exc L5 THEMIS SLC22A18
##                                             predicted.subclass.score
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                0.8557476
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                1.0000000
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                0.9240861
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                0.9498290
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                1.0000000
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                1.0000000
##                                             predicted.subclass
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1            L2/3 IT
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1              L5 IT
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1              Pvalb
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1              L6 IT
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1              L6 CT
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1              L5 IT
##                                             predicted.cross_species_cluster.score
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             0.8240176
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             0.9845528
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             0.7955298
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             0.5529920
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             1.0000000
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             0.9873519
##                                             predicted.cross_species_cluster
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                         L2/3 IT
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                         L5 IT_2
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                         Pvalb_1
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                         L6 IT_1
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                         L6 CT_2
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                         L5 IT_2
##                                             mapping.score SCT_snn_res.0.8
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1     0.9784835               7
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1     1.0000000              11
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1     1.0000000              15
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1     0.7423896               6
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1     0.9711277              13
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1     0.9881113              11
##                                             seurat_clusters atac_doublets
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1               7       singlet
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1              11       singlet
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1              15       singlet
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1               6       singlet
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1              13       singlet
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1              11       singlet
##                                             pANN_0.25_0.01_374
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1          0.2696629
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1          0.1797753
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1          0.1348315
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1          0.1123596
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1          0.1123596
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1          0.2808989
##                                             DF.classifications_0.25_0.01_374
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                          Singlet
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                          Singlet
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                          Singlet
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                          Singlet
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                          Singlet
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                          Singlet
##                                             rna_doublets all_doublets region.x
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1      singlet      singlet    DLPFC
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1      singlet      singlet    DLPFC
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1      singlet      singlet    DLPFC
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1      singlet      singlet    DLPFC
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1      singlet      singlet    DLPFC
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1      singlet      singlet    DLPFC
##                                             pANN_0.25_0.01_198
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_198
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_409
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_409
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_6
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1               NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1               NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1               NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1               NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1               NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1               NA
##                                             DF.classifications_0.25_0.01_6
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                           <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                           <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                           <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                           <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                           <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                           <NA>
##                                             pANN_0.25_0.01_76
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_76
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_280
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_280
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_141
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_141
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_287
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_287
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_188
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_188
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_77
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_77
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_196
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_196
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_203
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_203
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_73
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_73
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_370
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_370
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_127
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_127
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_269
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_269
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_37
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_37
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_403
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_403
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_144
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_144
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_500
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_500
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_503
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_503
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_140
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_140
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_60
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_60
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_83
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_83
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_64
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_64
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_134
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_134
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_75
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_75
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                             pANN_0.25_0.01_193
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_193
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_182
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_182
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_120
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_120
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_186
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_186
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_183
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_183
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_115
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                 NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                 NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                 NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                 NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                 NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                 NA
##                                             DF.classifications_0.25_0.01_115
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                             <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                             <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                             <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                             <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                             <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                             <NA>
##                                             pANN_0.25_0.01_71
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                NA
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                NA
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                NA
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                NA
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                NA
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                NA
##                                             DF.classifications_0.25_0.01_71
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1                            <NA>
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1                            <NA>
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1                            <NA>
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1                            <NA>
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1                            <NA>
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1                            <NA>
##                                                               sample
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 1041-Schizophrenia-DLPFC
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 1041-Schizophrenia-DLPFC
##                                                 condition region.y donor batch
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 Schizophrenia    DLPFC  1041    16
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 Schizophrenia    DLPFC  1041    16
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 Schizophrenia    DLPFC  1041    16
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 Schizophrenia    DLPFC  1041    16
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 Schizophrenia    DLPFC  1041    16
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 Schizophrenia    DLPFC  1041    16
##                                                sex  age
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 Female 36.7
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 Female 36.7
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 Female 36.7
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 Female 36.7
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 Female 36.7
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 Female 36.7
##                                                                  race source
## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 Black or African-American   Joan
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 Black or African-American   Joan
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 Black or African-American   Joan
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 Black or African-American   Joan
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 Black or African-American   Joan
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 Black or African-American   Joan

Preprocessing without batch correction

Idents(obj) <- 'sample'

RNA

# normalize data using the standard scaling/log-transform
DefaultAssay(obj) <- "RNA"

obj <- NormalizeData(obj, normalization.method = "LogNormalize", 
                     scale.factor = 10000)

# find variable genes and scale data
obj <- FindVariableFeatures(obj, selection.method = "vst", nfeatures = 2000)

# Identify the 10 most highly variable genes
top10 <- head(VariableFeatures(obj), 10)

# SCT
obj <- SCTransform(obj,
                    new.assay.name = "SCT",
                    verbose = T)

## Calculating cell attributes from input UMI matrix: log_umi

## Variance stabilizing transformation of count matrix of size 33781 by 155745

## Model formula is y ~ log_umi

## Get Negative Binomial regression parameters per gene

## Using 2000 genes, 5000 cells

##   |                                                                              |                                                                      |   0%  |                                                                              |==================                                                    |  25%  |                                                                              |===================================                                   |  50%  |                                                                              |====================================================                  |  75%  |                                                                              |======================================================================| 100%

## Found 100 outliers - those will be ignored in fitting/regularization step

## Second step: Get residuals using fitted parameters for 33781 genes

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                                                              |====                                                                  |   6%  |                                                                              |=====                                                                 |   7%  |                                                                              |======                                                                |   9%  |                                                                              |=======                                                               |  10%  |                                                                              |========                                                              |  12%  |                                                                              |=========                                                             |  13%  |                                                                              |==========                                                            |  15%  |                                                                              |===========                                                           |  16%  |                                                                              |============                                                          |  18%  |                                                                              |=============                                                         |  19%  |                                                                              |==============                                                        |  21%  |                                                                              |===============                                                       |  22%  |                                                                              |================                                                      |  24%  |                                                                              |==================                                                    |  25%  |                                                                              |===================                                                   |  26%  |                                                                              |====================                                                  |  28%  |                                                                              |=====================                                                 |  29%  |                                                                              |======================                                                |  31%  |                                                                              |=======================                                               |  32%  |                                                                              |========================                                              |  34%  |                                                                              |=========================                                             |  35%  |                                               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## Computing corrected count matrix for 33781 genes

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## Calculating gene attributes

## Wall clock passed: Time difference of 17.80086 mins

## Determine variable features

## Place corrected count matrix in counts slot

## Centering data matrix

## Set default assay to SCT

obj <- RunPCA(obj,
              assay = "SCT",
              reduction.name = 'pca',
              reduction.key = "PC"
            )

## PC_ 1 
## Positive:  ST18, CTNNA3, RNF220, MBP, MOBP, AC008571.2, LINC01608, AC012494.1, PLP1, SLC7A14-AS1 
##     TMEM144, KCNH8, FRMD4B, SLC5A11, TF, DOCK5, C10orf90, DOCK10, ENPP2, PIP4K2A 
##     LINC00609, AL033523.1, QKI, LINC01170, LPAR1, COL4A5, SHROOM4, AC079352.1, ABCA8, UGT8 
## Negative:  KCNIP4, GPC5, SLC1A2, ROBO2, DPP10, GRIK1, ADGRV1, RBFOX1, NXPH1, CSMD1 
##     HPSE2, OBI1-AS1, SGCZ, CNTN5, ZNF385D, NKAIN3, LHFPL3, CNTNAP2, SYT1, ADARB2 
##     NRXN1, LRRTM4, CTNNA2, NRG3, RALYL, PCDH15, GPM6A, DLGAP1, AC109466.1, OPCML 
## PC_ 2 
## Positive:  GPC5, SLC1A2, ADGRV1, SLC1A3, OBI1-AS1, HPSE2, LINC00499, AC002429.2, NKAIN3, AL137139.2 
##     ARHGAP24, ZNF98, BMPR1B, NHSL1, PITPNC1, PREX2, RFX4, PARD3B, SLC4A4, FAM189A2 
##     NEAT1, RANBP3L, GNA14, GPM6A, RYR3, AC012405.1, SLC14A1, PARD3, SLCO1C1, LINC00299 
## Negative:  KCNIP4, ROBO2, RBFOX1, GRIK1, CSMD1, ADARB2, CNTNAP2, SYT1, CNTN5, NXPH1 
##     RALYL, SGCZ, AC109466.1, ZNF385D, IL1RAPL2, LRRTM4, NRG1, DLGAP1, OPCML, KCNQ5 
##     FGF14, ATRNL1, IQCJ-SCHIP1, GALNTL6, CCSER1, KIAA1217, HS6ST3, STXBP5L, SNHG14, GRIK2 
## PC_ 3 
## Positive:  LRMDA, DOCK8, APBB1IP, ADAM28, AL163541.1, LNCAROD, FYB1, TBXAS1, P2RY12, LINC01374 
##     ARHGAP24, LINC02712, PLXDC2, ST6GAL1, INPP5D, AC008691.1, PTPRC, RUNX1, ARHGAP15, C3 
##     SLCO2B1, SYK, DLEU1, DOCK2, SAMSN1, CPED1, CSF1R, BLNK, IKZF1, LPAR6 
## Negative:  GPC5, SLC1A2, ADGRV1, OBI1-AS1, HPSE2, NKAIN3, AC002429.2, LINC00499, DPP10, ERBB4 
##     ZNF98, AL137139.2, GPM6A, PITPNC1, BMPR1B, PREX2, SLC4A4, CTNNA2, RYR3, RFX4 
##     NPAS3, FBXL7, ADARB2, PARD3, RANBP3L, LSAMP, LINC00299, FAM189A2, AC012405.1, PTPRZ1 
## PC_ 4 
## Positive:  LHFPL3, ADARB2, PCDH15, NXPH1, GRIK1, AC004852.2, VCAN, SOX6, ERBB4, SGCZ 
##     ZNF385D, LUZP2, PTPRZ1, BX284613.2, KCNMB2, MEGF11, SEMA5A, PDGFRA, TNR, RELN 
##     GRIP1, ALK, MYO16, DSCAM, SLC24A3, LRRC4C, SMOC1, DLX6-AS1, KCNIP1, FGF13 
## Negative:  KCNIP4, AC109466.1, AC060765.2, RALYL, AC073091.3, AC013287.1, AC011287.1, IL1RAPL2, AL117329.1, AC034268.2 
##     IQCJ-SCHIP1, CBLN2, TAFA1, LINC02306, AJ009632.2, AC008415.1, LINC02055, LDB2, CADPS2, CASC15 
##     AC019211.1, LINC01378, KCNQ5, NRG1, FSTL4, AL157944.1, RORB, PHACTR1, CPNE4, SYT1 
## PC_ 5 
## Positive:  LHFPL3, PCDH15, AC004852.2, VCAN, BX284613.2, PTPRZ1, TNR, DSCAM, SEMA5A, KCNIP4 
##     MEGF11, CA10, PDGFRA, XYLT1, LUZP2, MIR3681HG, SMOC1, LRRC4C, COL9A1, MMP16 
##     FERMT1, STK32A, OPCML, SOX6, AC124254.2, DCC, KCNMB2, PDZD2, AL445250.1, MAML2 
## Negative:  ADARB2, GRIK1, ZNF385D, ERBB4, RELN, GRIP1, SGCZ, CNTN5, ROBO2, FGF13 
##     DLX6-AS1, NXPH1, AC132803.1, GALNTL6, FSTL5, CNTNAP2, GAD2, PRELID2, THSD7B, EYA4 
##     SYNPR, BTBD11, SLC35F4, C8orf34, KIT, PTPRM, MYO16, NR2F2-AS1, PTCHD4, GRIN3A

ElbowPlot(obj,
         reduction = "pca")

ATAC

DefaultAssay(obj) <- "ATAC"

obj <- FindTopFeatures(obj)
obj <- RunTFIDF(obj)

## Performing TF-IDF normalization

obj <- RunSVD(obj,
              reduction.key = "LSI",
              reduction.name = "lsi")

## Running SVD

## Scaling cell embeddings

DefaultAssay(obj) <- "ATAC"
DepthCor(obj,
        reduction = "lsi")

obj

## An object of class Seurat 
## 417826 features across 155745 samples within 3 assays 
## Active assay: ATAC (347444 features, 330250 variable features)
##  2 layers present: counts, data
##  2 other assays present: RNA, SCT
##  2 dimensional reductions calculated: pca, lsi

Dimensionality reduction and clustering

# build a joint neighbor graph using both assays
obj <- FindMultiModalNeighbors(
  object = obj,
  reduction.list = list("pca", "lsi"),
  knn.graph.name = "wknn",
  snn.graph.name = "wsnn",
  weighted.nn.name = "weighted.nn",
  dims.list = list(1:50, 2:50),
  verbose = TRUE
)

## Calculating cell-specific modality weights

## Finding 20 nearest neighbors for each modality.

## Calculating kernel bandwidths

## Finding multimodal neighbors

## Constructing multimodal KNN graph

## Constructing multimodal SNN graph

# build a joint UMAP visualization
obj <- RunUMAP(
  object = obj,
  nn.name = "weighted.nn",
  reduction.name = "wnn.umap",
  reduction.key = "wnnUMAP_",
  verbose = TRUE
)

## 05:34:49 UMAP embedding parameters a = 0.9922 b = 1.112

## 05:34:51 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 05:34:52 3 smooth knn distance failures
## 05:34:55 Initializing from normalized Laplacian + noise (using irlba)
## 05:35:12 Commencing optimization for 200 epochs, with 5020758 positive edges
## 05:36:31 Optimization finished

# cluster over neighbor graph
obj <- FindClusters(
  object = obj,
  algorithm = 4,
  resolution = 0.6,
  graph.name = 'wsnn',
  verbose = TRUE,
  method = "igraph"
)

## 50 singletons identified. 42 final clusters.

DimPlot(obj,
        pt.size = 1,
        label.size = 0,
        reduction = "wnn.umap",
        group.by = 'batch',
        raster = TRUE)

## Rasterizing points since number of points exceeds 100,000.
## To disable this behavior set `raster=FALSE`

# barplot of cluster breakdown by sample
obj@meta.data %>%
    ggplot(aes(x = seurat_clusters)) +
    geom_bar(aes(fill = sample), position = "fill") +
    ggtitle("Breakdown of clusters by sample")

# barplot of cluster breakdown by batch
obj@meta.data %>%
    mutate(batch = factor(batch)) %>% 
    ggplot(aes(x = seurat_clusters)) +
    geom_bar(aes(fill = batch), position = "fill") +
    ggtitle("Breakdown of clusters by batch")

Run Harmony batch correction using batch column

obj@meta.data$batch <- as.factor(obj@meta.data$batch)
DefaultAssay(obj) <- "SCT"

obj_harmony <- RunHarmony(
    object = obj,
    group.by.vars = 'batch',
    reduction = 'pca',
    assay.use = 'SCT',
    reduction.save = "harmony_sct_batch",
    project.dim = FALSE
)

## Transposing data matrix

## Initializing state using k-means centroids initialization

## Harmony 1/10

## Harmony 2/10

## Harmony 3/10

## Harmony 4/10

## Harmony 5/10

## Harmony 6/10

## Harmony converged after 6 iterations

DefaultAssay(obj_harmony) <- "ATAC"

obj_harmony <- RunHarmony(
    object = obj_harmony,
    group.by.vars = 'batch',
    reduction = 'lsi',
    assay.use = 'ATAC',
    reduction.save = "harmony_atac_batch",
    project.dim = FALSE
)

## Transposing data matrix

## Initializing state using k-means centroids initialization

## Harmony 1/10

## Harmony 2/10

## Harmony 3/10

## Harmony 4/10

## Harmony 5/10

## Harmony 6/10

## Harmony 7/10

## Harmony 8/10

## Harmony 9/10

## Harmony 10/10

# build a joint neighbor graph using both assays
obj_harmony <- FindMultiModalNeighbors(
  object = obj_harmony,
  reduction.list = list("harmony_sct_batch", "harmony_atac_batch"),
  knn.graph.name = "wknn_batch",
  snn.graph.name = "wsnn_batch",
  weighted.nn.name = "weighted.nn_batch",
  dims.list = list(1:50, 2:50),
  verbose = TRUE
)

## Calculating cell-specific modality weights

## Finding 20 nearest neighbors for each modality.

## Calculating kernel bandwidths

## Finding multimodal neighbors

## Constructing multimodal KNN graph

## Constructing multimodal SNN graph

# build a joint UMAP visualization
obj_harmony <- RunUMAP(
  object = obj_harmony,
  nn.name = "weighted.nn_batch",
  reduction.name = "harm.wnn.umap_batch",
  reduction.key = "harm.batch.wnnUMAP_",
  verbose = TRUE
)

## 06:01:36 UMAP embedding parameters a = 0.9922 b = 1.112

## 06:01:39 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 06:01:40 2 smooth knn distance failures
## 06:01:43 Initializing from normalized Laplacian + noise (using irlba)
## 06:02:06 Commencing optimization for 200 epochs, with 5148778 positive edges
## 06:03:22 Optimization finished

Azimuth

DefaultAssay(obj_harmony) <- "SCT"

obj_harmony <- RunAzimuth(obj_harmony, 
                          reference = "humancortexref", 
                          assay="SCT",
                          umap.name = "ref.umap") 

## detected inputs from HUMAN with id type Gene.name

## reference rownames detected HUMAN with id type Gene.name

## Using reference SCTModel to calculate pearson residuals

## Determine variable features

## Setting min_variance to:  -Inf

## Calculating residuals of type pearson for 2216 genes

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## Set default assay to refAssay

## Normalizing query using reference SCT model

## Projecting cell embeddings

## Finding query neighbors

## Finding neighborhoods

## Finding anchors

##  Found 22152 anchors

## Finding integration vectors

## Finding integration vector weights

## Predicting cell labels
## Predicting cell labels
## Predicting cell labels
## Predicting cell labels

## 
## Integrating dataset 2 with reference dataset

## Finding integration vectors

## Integrating data

## Computing nearest neighbors

## Running UMAP projection

## 06:09:56 Read 155745 rows

## 06:09:56 Processing block 1 of 1

## 06:09:56 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 20
## 06:09:57 Initializing by weighted average of neighbor coordinates using 1 thread
## 06:09:57 Commencing optimization for 67 epochs, with 3114900 positive edges
## 06:10:12 Finished
## Projecting reference PCA onto query
## Finding integration vector weights
## Projecting back the query cells into original PCA space
## Finding integration vector weights
## Computing scores:
##     Finding neighbors of original query cells
##     Finding neighbors of transformed query cells
##     Computing query SNN
##     Determining bandwidth and computing transition probabilities
## Total elapsed time: 1.99347029129664

obj_harmony

## An object of class Seurat 
## 451804 features across 155745 samples within 8 assays 
## Active assay: refAssay (33781 features, 2216 variable features)
##  3 layers present: counts, data, scale.data
##  7 other assays present: RNA, ATAC, SCT, prediction.score.class, prediction.score.cluster, prediction.score.subclass, prediction.score.cross_species_cluster
##  8 dimensional reductions calculated: pca, lsi, wnn.umap, harmony_sct_batch, harmony_atac_batch, harm.wnn.umap_batch, integrated_dr, ref.umap

DimPlot(obj_harmony, shuffle=TRUE, label = FALSE, repel = TRUE, pt.siz=1, 
        label.size=0, reduction = "harm.wnn.umap_batch", 
        group.by = 'predicted.subclass', raster=FALSE) + 
  theme(legend.text = element_text(size=30), 
        plot.title = element_text(size=40), 
        axis.title = element_text(size=30)
        )

Leiden clustering

obj_harmony <- FindClusters(
  object = obj_harmony,
  algorithm = 4,
  resolution = 0.6,
  graph.name = 'wsnn_batch',
  verbose = TRUE,
  method = "igraph"
)

## 88 singletons identified. 36 final clusters.

table(obj_harmony$seurat_clusters)

## 
##     1     2     3     4     5     6     7     8     9    10    11    12    13 
## 34299 15128 12782  9130  8707  8525  7786  6335  5942  5565  4467  4372  4036 
##    14    15    16    17    18    19    20    21    22    23    24    25    26 
##  3992  2493  2362  2038  1979  1857  1801  1464  1415  1204  1119  1097  1060 
##    27    28    29    30    31    32    33    34    35    36 
##  1021   867   858   755   668   499   113     4     3     2

head(obj_harmony$seurat_clusters)

## 1041-Schizophrenia-DLPFC_GCTGAGGAGTATTGCA-1 
##                                           7 
## 1041-Schizophrenia-DLPFC_ACACTTGCAATAGCCC-1 
##                                           9 
## 1041-Schizophrenia-DLPFC_ATAGCATGTCCTTCTC-1 
##                                          13 
## 1041-Schizophrenia-DLPFC_TCTAACCGTTTCCACG-1 
##                                          11 
## 1041-Schizophrenia-DLPFC_CATAGTCAGCGCATTG-1 
##                                          18 
## 1041-Schizophrenia-DLPFC_AGTAATCGTTGAGGTC-1 
##                                           9 
## 36 Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 ... 36

# sanity check
# https://www.geeksforgeeks.org/check-if-two-objects-are-equal-in-r-programming-setequal-function/
setequal(Idents(obj_harmony), obj_harmony@meta.data$seurat_cluster)

## [1] TRUE

setequal(obj_harmony@meta.data$seurat_clusters, 
         obj_harmony@meta.data$seurat_cluster)

## [1] TRUE

DimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1, 
        label.size=0, reduction = "harm.wnn.umap_batch", 
        group.by = 'seurat_clusters', raster=FALSE) + 
  theme(legend.text = element_text(size=30), 
        plot.title = element_text(size=40),
        axis.title = element_text(size=30)
        )

Visualize batch-corrected data

# barplot of cluster breakdown by sample
obj_harmony@meta.data %>%
    ggplot(aes(x = seurat_clusters)) +
    geom_bar(aes(fill = sample), position = "fill") +
    ggtitle("Breakdown of clusters by sample")

# barplot of cluster breakdown by batch
obj_harmony@meta.data %>%
    mutate(batch = factor(batch)) %>% 
    ggplot(aes(x = seurat_clusters)) +
    geom_bar(aes(fill = batch), position = "fill") +
    ggtitle("Breakdown of clusters by batch")

By condition

# batch
DimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1, 
        label.size=0, reduction = "harm.wnn.umap_batch", group.by = 'condition', 
        raster=FALSE) + theme(legend.text = element_text(size=30), 
                              plot.title = element_text(size=40), 
                              axis.title = element_text(size=30)
                              )

By sample

# batch
DimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1, 
        label.size=0, reduction = "harm.wnn.umap_batch", group.by = 'sample', 
        raster=FALSE) + theme(plot.title = element_text(size=40), 
                              axis.title = element_text(size=30))

By ‘batch’

DimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1, 
        label.size=0, reduction = "harm.wnn.umap_batch", group.by = 'batch', 
        raster=FALSE) + theme(plot.title = element_text(size=40), 
                              axis.title = element_text(size=30))

Assign majority celltype per cluster

df_cluster_celltype <- obj_harmony@meta.data %>% 
  dplyr::select(seurat_clusters, predicted.subclass) %>% 
  group_by(seurat_clusters, predicted.subclass) %>%
  summarise(n = n()) %>% 
  top_n(1, n)

## `summarise()` has grouped output by 'seurat_clusters'. You can override using
## the `.groups` argument.

df_cluster_celltype

## # A tibble: 36 × 3
## # Groups:   seurat_clusters [36]
##    seurat_clusters predicted.subclass     n
##    <fct>           <chr>              <int>
##  1 1               Oligo              34297
##  2 2               Oligo              15124
##  3 3               Astro              12702
##  4 4               OPC                 9082
##  5 5               L2/3 IT             8552
##  6 6               Micro-PVM           8421
##  7 7               L2/3 IT             7500
##  8 8               Astro               6268
##  9 9               L5 IT               5891
## 10 10              Sst                 5344
## # ℹ 26 more rows

obj_harmony@meta.data$predicted.cell_type_percluster <- plyr::mapvalues(
  obj_harmony@meta.data$seurat_clusters, 
  from = df_cluster_celltype$seurat_clusters,
  to = df_cluster_celltype$predicted.subclass)

Idents(obj_harmony) <- "predicted.cell_type_percluster"

DimPlot(obj_harmony, shuffle=TRUE, label = TRUE, repel = TRUE, pt.siz=1, 
        label.size=0, reduction = "harm.wnn.umap_batch", 
        group.by = 'predicted.cell_type_percluster', raster=FALSE) + 
  theme(legend.text = element_text(size=30),
        plot.title = element_text(size=40),
        axis.title = element_text(size=30)
        )

Visualize marker genes

DefaultAssay(obj_harmony) <- "SCT"

FeaturePlot(
  object = obj_harmony,
  features = c("PLP1",    # Oligodendrocytes
               "AQP4",    # Astrocytes
               "C1QC",    # Microglia
               "SV2B",    # Excitatory Neurons
               "GAD1",    # Inhibitory Neurons
               "PDGFRA"), # OPCs),
  pt.size = 0.2,
  label.size = 4,
  max.cutoff = 'q95',
  ncol = 3,
  reduction = "harm.wnn.umap_batch",
  label = TRUE,
  raster = FALSE,
  order = TRUE
)

Save objects

saveRDS(obj_harmony, file = paste0(data_dir, "/", brain_region, 
                                   ".integrated.batch.analyzed.rds"))
cell_metadata <- obj_harmony@meta.data
saveRDS(cell_metadata, file = paste0(
  data_dir, "/", brain_region, ".integrated.batch.analyzed.cell_metadata.rds"))

Session info

sessionInfo()

## R version 4.2.0 (2022-04-22)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/libf77blas.so.3.10.3
## LAPACK: /users/guozy/miniconda3/envs/psych/lib/libopenblasp-r0.3.27.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] RColorBrewer_1.1-3                glue_1.6.2                       
##  [3] data.table_1.14.8                 harmony_1.1.0                    
##  [5] Rcpp_1.0.11                       BSgenome.Hsapiens.UCSC.hg38_1.4.5
##  [7] BSgenome_1.66.3                   rtracklayer_1.58.0               
##  [9] Biostrings_2.66.0                 XVector_0.38.0                   
## [11] EnsDb.Hsapiens.v86_2.99.0         ensembldb_2.22.0                 
## [13] AnnotationFilter_1.22.0           GenomicFeatures_1.50.4           
## [15] AnnotationDbi_1.60.2              Biobase_2.58.0                   
## [17] GenomicRanges_1.50.2              GenomeInfoDb_1.34.9              
## [19] IRanges_2.32.0                    S4Vectors_0.36.2                 
## [21] BiocGenerics_0.44.0               Azimuth_0.4.6                    
## [23] shinyBS_0.61.1                    Signac_1.9.0                     
## [25] SeuratObject_5.0.0                Seurat_4.3.0                     
## [27] viridis_0.6.4                     viridisLite_0.4.2                
## [29] readr_2.1.4                       purrr_1.0.2                      
## [31] ggplot2_3.5.1                     dplyr_1.1.2                      
## [33] tidyr_1.3.0                      
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.4                      shinydashboard_0.7.2           
##   [3] spatstat.explore_3.2-7          reticulate_1.37.0              
##   [5] tidyselect_1.2.1                RSQLite_2.3.7                  
##   [7] htmlwidgets_1.6.4               grid_4.2.0                     
##   [9] BiocParallel_1.32.6             Rtsne_0.17                     
##  [11] munsell_0.5.1                   codetools_0.2-20               
##  [13] ica_1.0-3                       DT_0.33                        
##  [15] future_1.33.2                   miniUI_0.1.1.1                 
##  [17] withr_3.0.0                     spatstat.random_3.2-3          
##  [19] colorspace_2.1-0                progressr_0.14.0               
##  [21] filelock_1.0.3                  highr_0.11                     
##  [23] knitr_1.47                      ROCR_1.0-11                    
##  [25] tensor_1.5                      listenv_0.9.1                  
##  [27] labeling_0.4.3                  MatrixGenerics_1.10.0          
##  [29] GenomeInfoDbData_1.2.9          polyclip_1.10-6                
##  [31] farver_2.1.2                    bit64_4.0.5                    
##  [33] rprojroot_2.0.4                 parallelly_1.37.1              
##  [35] vctrs_0.6.5                     generics_0.1.3                 
##  [37] xfun_0.44                       BiocFileCache_2.6.1            
##  [39] R6_2.5.1                        humancortexref.SeuratData_1.0.0
##  [41] hdf5r_1.3.10                    DelayedArray_0.24.0            
##  [43] bitops_1.0-7                    spatstat.utils_3.0-4           
##  [45] cachem_1.1.0                    BiocIO_1.8.0                   
##  [47] promises_1.3.0                  scales_1.3.0                   
##  [49] googlesheets4_1.1.1             gtable_0.3.5                   
##  [51] globals_0.16.3                  goftest_1.2-3                  
##  [53] spam_2.9-1                      rlang_1.1.4                    
##  [55] RcppRoll_0.3.0                  splines_4.2.0                  
##  [57] lazyeval_0.2.2                  gargle_1.5.2                   
##  [59] spatstat.geom_3.2-9             yaml_2.3.8                     
##  [61] reshape2_1.4.4                  abind_1.4-5                    
##  [63] httpuv_1.6.15                   SeuratDisk_0.0.0.9021          
##  [65] tools_4.2.0                     SeuratData_0.2.2.9001          
##  [67] jquerylib_0.1.4                 ggridges_0.5.6                 
##  [69] plyr_1.8.9                      progress_1.2.3                 
##  [71] zlibbioc_1.44.0                 RCurl_1.98-1.14                
##  [73] prettyunits_1.2.0               deldir_2.0-4                   
##  [75] pbapply_1.7-2                   cowplot_1.1.3                  
##  [77] zoo_1.8-12                      SummarizedExperiment_1.28.0    
##  [79] ggrepel_0.9.5                   cluster_2.1.6                  
##  [81] here_1.0.1                      fs_1.6.4                       
##  [83] magrittr_2.0.3                  scattermore_1.2                
##  [85] lmtest_0.9-40                   RANN_2.6.1                     
##  [87] googledrive_2.1.1               ProtGenerics_1.30.0            
##  [89] fitdistrplus_1.1-11             matrixStats_1.0.0              
##  [91] hms_1.1.3                       patchwork_1.2.0                
##  [93] shinyjs_2.1.0                   mime_0.12                      
##  [95] evaluate_0.24.0                 xtable_1.8-4                   
##  [97] RhpcBLASctl_0.23-42             XML_3.99-0.16.1                
##  [99] gridExtra_2.3                   compiler_4.2.0                 
## [101] biomaRt_2.54.1                  tibble_3.2.1                   
## [103] KernSmooth_2.23-20              crayon_1.5.2                   
## [105] htmltools_0.5.8.1               later_1.3.2                    
## [107] tzdb_0.4.0                      DBI_1.2.3                      
## [109] dbplyr_2.5.0                    MASS_7.3-56                    
## [111] rappdirs_0.3.3                  Matrix_1.6-1.1                 
## [113] cli_3.6.2                       parallel_4.2.0                 
## [115] dotCall64_1.1-1                 igraph_2.0.3                   
## [117] pkgconfig_2.0.3                 GenomicAlignments_1.34.1       
## [119] sp_2.1-4                        plotly_4.10.4                  
## [121] spatstat.sparse_3.0-3           xml2_1.3.6                     
## [123] bslib_0.7.0                     stringr_1.5.1                  
## [125] digest_0.6.35                   sctransform_0.4.0              
## [127] RcppAnnoy_0.0.22                spatstat.data_3.0-4            
## [129] rmarkdown_2.27                  cellranger_1.1.0               
## [131] leiden_0.4.3.1                  fastmatch_1.1-4                
## [133] uwot_0.2.2                      restfulr_0.0.15                
## [135] curl_5.2.1                      shiny_1.8.1.1                  
## [137] Rsamtools_2.14.0                rjson_0.2.21                   
## [139] lifecycle_1.0.4                 nlme_3.1-164                   
## [141] jsonlite_1.8.8                  fansi_1.0.6                    
## [143] pillar_1.9.0                    lattice_0.22-6                 
## [145] KEGGREST_1.38.0                 fastmap_1.2.0                  
## [147] httr_1.4.7                      survival_3.6-4                 
## [149] png_0.1-8                       bit_4.0.5                      
## [151] presto_1.0.0                    stringi_1.8.4                  
## [153] sass_0.4.9                      blob_1.2.4                     
## [155] memoise_2.0.1                   irlba_2.3.5.1                  
## [157] future.apply_1.11.2