# R script for Peak Model
#  -- generated by MACS
p <- c(0.0503086834906,0.0586758119027,0.0667781577701,0.0751982426912,0.0833005885586,0.0831946755408,0.0822944148888,0.0825591974335,0.0824003279067,0.0816059802726,0.0809175456565,0.0803879805671,0.0802291110403,0.0798584154777,0.0798584154777,0.0794347634062,0.0795406764241,0.0792229373705,0.0790111113347,0.0795406764241,0.0798054589688,0.0797525024598,0.0793818068973,0.078799285299,0.0785345027543,0.0785874592632,0.0784815462453,0.0782167637006,0.0781108506828,0.0774753725755,0.0769987639951,0.0772105900308,0.0781108506828,0.0783756332275,0.0785345027543,0.0790111113347,0.0794347634062,0.0795406764241,0.0794347634062,0.0795406764241,0.0797525024598,0.0793818068973,0.0788522418079,0.0791170243526,0.0789051983168,0.0785874592632,0.0786404157721,0.0783756332275,0.0783226767185,0.0781108506828,0.0778460681381,0.0783226767185,0.0783756332275,0.0784815462453,0.0788522418079,0.0785874592632,0.0782167637006,0.0784285897364,0.0785345027543,0.078799285299,0.0796995459509,0.0793818068973,0.0793818068973,0.0786933722811,0.0783226767185,0.0785345027543,0.0789051983168,0.0789051983168,0.0795406764241,0.0796995459509,0.0788522418079,0.0792758938794,0.0791699808615,0.0797525024598,0.0800172850045,0.080440937076,0.080493893585,0.0805998066028,0.0801761545313,0.0803350240581,0.080440937076,0.080493893585,0.0807057196207,0.080440937076,0.080493893585,0.0798584154777,0.0796995459509,0.0794877199151,0.0793288503883,0.0792758938794,0.079593632933,0.0790640678436,0.0792229373705,0.0796995459509,0.0799113719866,0.0801761545313,0.0802291110403,0.0806527631118,0.0809175456565,0.0807586761296,0.0808645891475,0.0812352847101,0.0809175456565,0.080440937076,0.0801761545313,0.0805998066028,0.0805468500939,0.0803879805671,0.080493893585,0.0806527631118,0.0803350240581,0.0801761545313,0.0800702415135,0.0803350240581,0.0803879805671,0.0799113719866,0.0802820675492,0.080493893585,0.0810764151833,0.0811293716922,0.0816589367816,0.0817648497995,0.0824003279067,0.0825062409246,0.0825062409246,0.0828239799782,0.0828769364871,0.0826651104514,0.0816589367816,0.0820825888531,0.081341197728,0.0816059802726,0.081341197728,0.0810764151833,0.0809705021654,0.0810234586743,0.0806527631118,0.0809175456565,0.0811823282011,0.0806527631118,0.0809175456565,0.0808645891475,0.0808645891475,0.0810764151833,0.0815000672548,0.0814471107458,0.0815530237637,0.0813941542369,0.0807586761296,0.0807057196207,0.0806527631118,0.0802291110403,0.0802291110403,0.0802820675492,0.0800702415135,0.0799113719866,0.0799113719866,0.0794877199151,0.0802291110403,0.0803879805671,0.080440937076,0.0808645891475,0.0808645891475,0.0807057196207,0.0806527631118,0.0805468500939,0.080440937076,0.0808645891475,0.0808116326386,0.0808645891475,0.0809705021654,0.0807057196207,0.0806527631118,0.0812352847101,0.0812352847101,0.081288241219,0.0810234586743,0.0809175456565,0.0811823282011,0.081288241219,0.081288241219,0.0815000672548,0.082135545362,0.0819237193263,0.0820296323441,0.0825062409246,0.0827710234693,0.0828239799782,0.082982849505,0.083035806014,0.0834594580855,0.0835124145944,0.0826121539425,0.0826121539425,0.0825591974335,0.0819237193263,0.0819766758352,0.0818178063084,0.0813941542369,0.0809175456565,0.0802291110403,0.0798584154777,0.0802291110403,0.0799643284956,0.0798054589688,0.0800702415135,0.0801231980224,0.0800172850045,0.0800172850045,0.0801231980224,0.0797525024598,0.0798054589688,0.079646589442,0.0798054589688,0.0798054589688,0.0799113719866,0.0798054589688,0.0806527631118,0.0809175456565,0.081288241219,0.0817118932905,0.0819766758352,0.0822944148888,0.0820296323441,0.0820296323441,0.0816589367816,0.0819237193263,0.0815530237637,0.0815000672548,0.0811823282011,0.0814471107458,0.0812352847101,0.0810764151833,0.0813941542369,0.0811293716922,0.0813941542369,0.0812352847101,0.0815000672548,0.081341197728,0.0809705021654,0.0810234586743,0.081341197728,0.0807586761296,0.080440937076,0.0809175456565,0.0809175456565,0.0808645891475,0.080440937076,0.0802820675492,0.0808645891475,0.0809175456565,0.0806527631118,0.0812352847101,0.0810764151833,0.0810764151833,0.0810234586743,0.0809175456565,0.0807586761296,0.0809705021654,0.0808116326386,0.0806527631118,0.0807586761296,0.080440937076,0.0811293716922,0.0806527631118,0.0810764151833,0.0812352847101,0.081288241219,0.0808645891475,0.0805468500939,0.0805468500939,0.0805468500939,0.0805998066028,0.0798054589688,0.0805468500939,0.0803879805671,0.0801231980224,0.0803350240581,0.0807057196207,0.0807057196207,0.080493893585,0.0805468500939,0.080440937076,0.0808116326386,0.0800702415135,0.079646589442,0.0800172850045,0.0796995459509,0.0792758938794,0.0794877199151,0.0800172850045,0.0801231980224,0.0801761545313,0.0798584154777,0.0800172850045,0.0800702415135,0.0798054589688,0.0802820675492,0.0808116326386,0.0805998066028,0.0800172850045,0.0798584154777,0.0798584154777,0.0802291110403,0.0799113719866,0.0802820675492,0.0807586761296,0.0808116326386,0.0811293716922,0.0816059802726,0.0820296323441,0.082188501871,0.082188501871,0.0827180669603,0.0835653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m <- 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ycorr <- 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altd  <- c(0, 46, 131, 201, 334, 445, 474, 545, 583)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('59-RGA-GSE59187/RGA_ChIP2-GSM1429898/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) : 0,46,131,201,334,445,474,545,583',bty='n')
dev.off()