# R script for Peak Model
#  -- generated by MACS
p <- c(0.0332247791001,0.0395105481191,0.0440003831326,0.0487895404804,0.0529800531596,0.0526807308254,0.0535786978281,0.0517827638227,0.0493881851488,0.0532793754939,0.0499868298173,0.0505854744858,0.0499868298173,0.0499868298173,0.0499868298173,0.0496875074831,0.0499868298173,0.0502861521515,0.0499868298173,0.0475922511434,0.0484902181461,0.0440003831326,0.0434017384641,0.0431024161299,0.0425037714614,0.0404085151218,0.0413064821245,0.0410071597902,0.0437010607984,0.0425037714614,0.0425037714614,0.0451976724695,0.0448983501353,0.0463949618065,0.0466942841407,0.0478915734776,0.0448983501353,0.0445990278011,0.0463949618065,0.0478915734776,0.0487895404804,0.0493881851488,0.0517827638227,0.0520820861569,0.0541773424966,0.0550753094993,0.0568712435047,0.0571705658389,0.0541773424966,0.0538780201624,0.0532793754939,0.0514834414885,0.0535786978281,0.0523814084912,0.0499868298173,0.0460956394722,0.0463949618065,0.045796317138,0.0466942841407,0.045796317138,0.0448983501353,0.045796317138,0.0419051267929,0.0425037714614,0.045796317138,0.0496875074831,0.0493881851488,0.0493881851488,0.0493881851488,0.0496875074831,0.05088479682,0.0535786978281,0.0544766648308,0.0514834414885,0.0487895404804,0.0481908958119,0.0472929288092,0.0478915734776,0.0463949618065,0.0466942841407,0.0440003831326,0.040707837456,0.0389119034506,0.0389119034506,0.0392112257848,0.0395105481191,0.0392112257848,0.0395105481191,0.040707837456,0.0422044491272,0.0460956394722,0.045796317138,0.0469936064749,0.0487895404804,0.0493881851488,0.0475922511434,0.0490888628146,0.0505854744858,0.0505854744858,0.0502861521515,0.0493881851488,0.0505854744858,0.0532793754939,0.0541773424966,0.0538780201624,0.0550753094993,0.0550753094993,0.0520820861569,0.0526807308254,0.0499868298173,0.0493881851488,0.0502861521515,0.0499868298173,0.0511841191542,0.0502861521515,0.0493881851488,0.0505854744858,0.0523814084912,0.0520820861569,0.0541773424966,0.0547759871651,0.0553746318335,0.0532793754939,0.0520820861569,0.0517827638227,0.0532793754939,0.0511841191542,0.0511841191542,0.0502861521515,0.0502861521515,0.0496875074831,0.0487895404804,0.0511841191542,0.0532793754939,0.0535786978281,0.0526807308254,0.0514834414885,0.0517827638227,0.0541773424966,0.0547759871651,0.0547759871651,0.0550753094993,0.0547759871651,0.0517827638227,0.0532793754939,0.0532793754939,0.0562725988362,0.0538780201624,0.0541773424966,0.0517827638227,0.0517827638227,0.0511841191542,0.0511841191542,0.0505854744858,0.0526807308254,0.0532793754939,0.0520820861569,0.0538780201624,0.0535786978281,0.0547759871651,0.0544766648308,0.0550753094993,0.0550753094993,0.0568712435047,0.0547759871651,0.0550753094993,0.0547759871651,0.0541773424966,0.0538780201624,0.0547759871651,0.0568712435047,0.0547759871651,0.0532793754939,0.0538780201624,0.0532793754939,0.0523814084912,0.0514834414885,0.05088479682,0.0511841191542,0.0514834414885,0.0490888628146,0.0520820861569,0.0532793754939,0.0532793754939,0.0535786978281,0.0544766648308,0.0568712435047,0.0571705658389,0.0577692105074,0.0556739541678,0.0550753094993,0.0517827638227,0.0493881851488,0.0472929288092,0.0493881851488,0.05088479682,0.0517827638227,0.0502861521515,0.0469936064749,0.0466942841407,0.0496875074831,0.0502861521515,0.0526807308254,0.0514834414885,0.0496875074831,0.0481908958119,0.0463949618065,0.0493881851488,0.0538780201624,0.0556739541678,0.0535786978281,0.0553746318335,0.0541773424966,0.0583678551759,0.0604631115155,0.0589664998444,0.0598644668471,0.0595651445128,0.0580685328416,0.0562725988362,0.0574698881732,0.0583678551759,0.061061756184,0.0607624338498,0.0574698881732,0.0580685328416,0.0577692105074,0.0574698881732,0.055973276502,0.0589664998444,0.0577692105074,0.0571705658389,0.0586671775101,0.0571705658389,0.0580685328416,0.0583678551759,0.0589664998444,0.0598644668471,0.0595651445128,0.0574698881732,0.0601637891813,0.0607624338498,0.055973276502,0.0556739541678,0.0577692105074,0.0592658221786,0.0589664998444,0.0598644668471,0.0601637891813,0.0619597231867,0.0622590455209,0.0598644668471,0.0631570125236,0.0637556571921,0.0628576901894,0.0619597231867,0.0616604008525,0.061061756184,0.0625583678552,0.0631570125236,0.0622590455209,0.0631570125236,0.0604631115155,0.0622590455209,0.0598644668471,0.0589664998444,0.0598644668471,0.0628576901894,0.0640549795264,0.0619597231867,0.0625583678552,0.0613610785182,0.0664495582002,0.0655515911975,0.0676468475372,0.0688441368741,0.0682454922056,0.0640549795264,0.0628576901894,0.066150235866,0.0670482028687,0.0682454922056,0.0667488805345,0.0682454922056,0.0673475252029,0.0697421038768,0.0715380378822,0.0727353272192,0.0745312612246,0.0742319388904,0.0721366825507,0.0751299058931,0.0745312612246,0.0745312612246,0.0757285505615,0.0742319388904,0.0715380378822,0.0748305835588,0.0742319388904,0.0739326165561,0.0769258398985,0.0760278728958,0.0784224515696,0.0769258398985,0.0808170302435,0.0790210962381,0.0826129642489,0.0778238069012,0.0793204185724,0.0802183855751,0.0799190632408,0.0826129642489,0.081415674912,0.0808170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m <- 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ycorr <- 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altd  <- c(154)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('33-SEP3-AP1-24581456/SEP3-ChIP-seq-2d-biological-replicate-1-GSM1279838/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) : 154',bty='n')
dev.off()