# R script for Peak Model
#  -- generated by MACS
p <- c(0.0427434465257,0.050099742722,0.0569752352452,0.0642834510741,0.0710147024955,0.0715435865358,0.071255104332,0.0714474258012,0.0716397472704,0.071255104332,0.0703415773534,0.070437738088,0.0708704613936,0.0703415773534,0.0702934969861,0.0693799700075,0.0695242111094,0.0695242111094,0.0697165325785,0.0698126933131,0.0703415773534,0.0702454166188,0.0693318896402,0.0695242111094,0.0699088540477,0.0698607736804,0.0693799700075,0.0695722914766,0.0690914878037,0.0696684522112,0.0704858184553,0.0703415773534,0.0704858184553,0.0706300595572,0.0705338988226,0.0710147024955,0.0717359080049,0.0718320687395,0.0715435865358,0.0718320687395,0.0705338988226,0.0702454166188,0.0708704613936,0.0705338988226,0.0709666221282,0.0706781399244,0.0710627828628,0.0710147024955,0.0716878276377,0.070774300659,0.0722167116779,0.07288983682,0.0731783190238,0.0735629619622,0.0731302386565,0.0734668012276,0.0724571135144,0.0725051938817,0.072072470576,0.072072470576,0.0711589435974,0.0703415773534,0.0701973362515,0.0700530951496,0.0699088540477,0.0693799700075,0.0695722914766,0.0692357289056,0.069139568171,0.0696684522112,0.0692357289056,0.069139568171,0.0688030055999,0.0692357289056,0.0698126933131,0.070437738088,0.0706300595572,0.0706300595572,0.0710147024955,0.0702454166188,0.0711589435974,0.0719763098414,0.0723128724125,0.0720243902087,0.0716878276377,0.0714474258012,0.0712070239647,0.0714474258012,0.0711108632301,0.0717359080049,0.0713031846993,0.070774300659,0.0707262202917,0.0708223810263,0.0710627828628,0.0709666221282,0.0707262202917,0.0706300595572,0.0710627828628,0.0706781399244,0.0706781399244,0.0711589435974,0.0706300595572,0.0701973362515,0.0699088540477,0.0701011755169,0.070774300659,0.0705819791899,0.0698607736804,0.0700050147823,0.0699088540477,0.0700050147823,0.0708223810263,0.0706781399244,0.0713512650666,0.0715916669031,0.0709666221282,0.070774300659,0.0713993454339,0.0715916669031,0.0717839883722,0.070774300659,0.0701973362515,0.0706300595572,0.069956934415,0.0694280503748,0.0701492558842,0.0707262202917,0.070437738088,0.070437738088,0.0707262202917,0.0713512650666,0.0718320687395,0.0723128724125,0.072553274249,0.0728417564527,0.0725051938817,0.0723609527798,0.072553274249,0.0716397472704,0.0713031846993,0.0714474258012,0.0715435865358,0.0718320687395,0.0719282294741,0.0724090331471,0.0729859975546,0.0734668012276,0.0736591226968,0.0742360871043,0.0743322478389,0.075005372981,0.0745726496754,0.074188006737,0.074188006737,0.074188006737,0.0735148815949,0.0733225601257,0.073370640493,0.0739476049005,0.0735629619622,0.0727936760855,0.0731783190238,0.07288983682,0.0726013546163,0.0726494349836,0.0730821582892,0.0729859975546,0.0728417564527,0.0722167116779,0.0722167116779,0.0719282294741,0.0713993454339,0.0711108632301,0.0713512650666,0.070774300659,0.0702454166188,0.0706300595572,0.0706781399244,0.0710627828628,0.0716397472704,0.0722647920452,0.0726975153509,0.0733225601257,0.0727936760855,0.0731302386565,0.0737552834314,0.0732263993911,0.073370640493,0.0731783190238,0.0736110423295,0.0735629619622,0.0732263993911,0.0725051938817,0.0727455957182,0.0724571135144,0.0722647920452,0.0721686313106,0.0717359080049,0.0717359080049,0.0709185417609,0.070774300659,0.0708704613936,0.0710627828628,0.0716878276377,0.0722167116779,0.0717359080049,0.0720243902087,0.0725051938817,0.072553274249,0.0730821582892,0.0729379171873,0.0731783190238,0.0733225601257,0.0726975153509,0.0724571135144,0.07288983682,0.0724571135144,0.0716878276377,0.0716397472704,0.0713512650666,0.0716878276377,0.0718320687395,0.0714955061685,0.071255104332,0.0704858184553,0.0696684522112,0.0700050147823,0.0702454166188,0.0704858184553,0.0703896577207,0.0700050147823,0.0696203718439,0.070437738088,0.0713512650666,0.0717359080049,0.0724090331471,0.0723609527798,0.0726013546163,0.072553274249,0.0733225601257,0.0735629619622,0.0738033637987,0.0731302386565,0.0725051938817,0.0725051938817,0.0727936760855,0.0725051938817,0.0730821582892,0.0729859975546,0.0724090331471,0.0722167116779,0.0723128724125,0.0727455957182,0.0730821582892,0.0735148815949,0.0734187208603,0.0732263993911,0.0726975153509,0.0731783190238,0.0731302386565,0.0734187208603,0.0738995245332,0.0740437656351,0.0740437656351,0.0749092122465,0.0747168907773,0.0758708195924,0.0762554625307,0.0758227392251,0.0761112214288,0.0762073821634,0.0758227392251,0.076303542898,0.0764477839999,0.0760150606943,0.0760631410615,0.0760631410615,0.0764477839999,0.0766881858364,0.077120909142,0.077120909142,0.077120909142,0.0768324269383,0.0769766680402,0.0768805073056,0.0775055520804,0.0775055520804,0.0764477839999,0.0763997036326,0.0763516232653,0.0761593017961,0.0758227392251,0.0754380962867,0.0756304177559,0.0756784981232,0.0753419355521,0.075005372981,0.0760150606943,0.0761112214288,0.0758708195924,0.075966980327,0.0766881858364,0.0771689895093,0.076784346571,0.0765439447345,0.0770247484075,0.077120909142,0.0766881858364,0.0771689895093,0.0776978735496,0.0778901950188,0.0769766680402,0.0766881858364,0.0766401054691,0.0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m <- 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ycorr <- 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altd  <- c(153)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('15-PIF5ox-GSE35059/PIF5ox-shade-ChIPSeq-GSM861508/all.1x36mers.TAIR10.unique.MACS2_model.pdf',height=6,width=6)
plot(x,p,type='l',col=c('red'),main='Peak Model',xlab='Distance to the middle',ylab='Percentage')
lines(x,m,col=c('blue'))
legend('topleft',c('forward tags','reverse tags'),lty=c(1,1,1),col=c('red','blue'))
plot(xcorr,ycorr,type='l',col=c('black'),main='Cross-Correlation',xlab='Lag between + and - tags',ylab='Correlation')
abline(v=altd,lty=2,col=c('red'))
legend('topleft','alternative lag(s)',lty=2,col='red')
legend('right','alt lag(s) : 153',bty='n')
dev.off()