data <- list(x=10)
if(is.null(data$y))
is.null(data$y)
is.null(data$y) & data$y<3
is.null(data$y) & sqrt(data$y)<3
is.null(data$y) && sqrt(data$y)<3
!is.null(data$y) && sqrt(data$y)<3
!is.null(data$y) && sqrt(data$y)<3
data$y <- 2
!is.null(data$y) && sqrt(data$y)<3
data$y <- 10
!is.null(data$y) && sqrt(data$y)<3
getwd()
setwd("../../../")
list.files()
setwd("example")
setwd("../example")
setwd("spp/example")
getwd()
setwd("example")
setwd("spp/package")
setwd("package")
setwd("example")
library(spp)
 > chip.data <- read.eland.tags("chip1862_hg18.txt");

  chip.data <- read.eland.tags("chip1862_hg18.txt");
input.data <- read.eland.tags("mock1862_hg18.txt");
chip.data <- select.informative.tags(chip.data)
input.data <- select.informative.tags(input.data)
 fdr <- 1e-2; 

library(snow)

cluster <- makeCluster(8)
 bp <- find.binding.positions(signal.data=chip.data,control.data=input.data,fdr=fdr,method=tag.wtd,whs=detection.window
.halfsize,cluster=cluster)
 bp <- find.binding.positions(signal.data=chip.data,control.data=input.data,fdr=fdr,method=tag.wtd,whs=detection.window.halfsize,cluster=cluster)
 bp <- find.binding.positions(signal.data=chip.data,control.data=input.data,fdr=fdr,method=tag.wtd,whs=300,cluster=cluster)
fdr
fdr <- 1e-4
 bp <- find.binding.positions(signal.data=chip.data,control.data=input.data,fdr=fdr,method=tag.wtd,whs=300,cluster=cluster)
getwd()
setwd("../test")
source("~/wald/spp/package/spp/R/zroutines.R")
debugger()
5
ls()
str(k)
is.null(k)
Q
source("~/wald/spp/package/spp/R/zroutines.R")
source("~/wald/spp/package/spp/R/zroutines.R")
?makeCluster
clusterCall(,source,"~/wald/spp/package/spp/R/zroutines.R")
clusterCall(cluster,source,"~/wald/spp/package/spp/R/zroutines.R")
clusterCall(cluster,source,"~/wald/spp/package/spp/R/zroutines.R")
source("~/wald/spp/package/spp/R/zroutines.R")
str(spp.bp)
str(spp.bp)
names(spp.bp)
names(spp.bp$npl)
names(spp.bp$npl[[1]])
str(spp.bp$npl[[1]])
setwd("../example")
bp <- find.binding.positions(signal.data=chip.data,control.data=input.data,fdr=fdr,method=tag.wtd,whs=300,cluster=cluster)
str(bp)
fdr <- 1e-2
bp <- find.binding.positions(signal.data=chip.data,control.data=input.data,fdr=fdr,method=tag.wtd,whs=300,cluster=cluster)
str(bp)
names(chip.treat)
table(names(chip.treat) %in% names(chip.control))
quit(save="no")
