# R script for Peak Model
#  -- generated by MACS
p <- c(0.044823015657,0.0525647246318,0.0606022950962,0.0675550400991,0.0750008875845,0.0748529568397,0.074507785102,0.074705026095,0.0756912310599,0.0768253667696,0.0786498459548,0.0791922586855,0.0787484664513,0.0805729456364,0.0791429484373,0.0787484664513,0.0777129512381,0.0768746770179,0.0761843335424,0.0762829540389,0.0745570953502,0.0730777879028,0.0733243391441,0.0713026189659,0.0726339956686,0.0730284776546,0.0747543363432,0.0760364027977,0.0753953695704,0.074705026095,0.075296749074,0.0774170897486,0.0769239872661,0.0766281257766,0.0772691590039,0.0772198487556,0.0764308847836,0.0768253667696,0.0774663999968,0.0759870925494,0.0758391618047,0.07371882113,0.0731764083993,0.0737681313783,0.0732750288958,0.0733243391441,0.0731764083993,0.0727326161651,0.0723381341791,0.0725846854203,0.0730284776546,0.0727819264133,0.0736695108818,0.0748036465915,0.074507785102,0.0732257186476,0.0725846854203,0.0732750288958,0.0731270981511,0.0723381341791,0.0705136549939,0.0722888239309,0.0722888239309,0.0715984804554,0.0719436521931,0.0728312366616,0.074310544109,0.0731764083993,0.0735708903853,0.0741626133643,0.0747543363432,0.0742119236125,0.0748529568397,0.0739653723713,0.0739653723713,0.0744584748537,0.0737681313783,0.0728312366616,0.0730284776546,0.074113303116,0.0751488183292,0.0759377823012,0.074902267088,0.0760364027977,0.0754939900669,0.0742612338608,0.074310544109,0.0757898515564,0.0757405413082,0.0757898515564,0.0754446798187,0.0748529568397,0.0745570953502,0.0745570953502,0.0756912310599,0.0766281257766,0.0767760565214,0.0753953695704,0.0753460593222,0.0745570953502,0.0742119236125,0.0740639928678,0.0725846854203,0.0708588267317,0.0709574472282,0.0709081369799,0.0709081369799,0.0724860649238,0.0718450316966,0.0723381341791,0.0723381341791,0.0710067574764,0.0732257186476,0.0751981285775,0.0742612338608,0.0740639928678,0.0733736493923,0.0720422726896,0.0735708903853,0.0726833059168,0.0727326161651,0.0734722698888,0.0728312366616,0.0728312366616,0.0730284776546,0.0738174416265,0.0740146826195,0.0751981285775,0.0752474388257,0.0760857130459,0.0775157102451,0.0783539844653,0.0782060537206,0.0791429484373,0.0785512254583,0.0790443279408,0.079488120175,0.0791429484373,0.0781074332241,0.0781074332241,0.0775650204933,0.0782060537206,0.0784526049618,0.0774170897486,0.0780581229758,0.0759377823012,0.0760857130459,0.0762829540389,0.0760857130459,0.0753953695704,0.0746557158467,0.0725353751721,0.0722395136826,0.0721902034344,0.0720422726896,0.0727819264133,0.073521580137,0.0741626133643,0.07371882113,0.074507785102,0.074705026095,0.0765295052801,0.0786005357065,0.0773677795003,0.0779595024793,0.0776143307416,0.0770226077626,0.0763322642872,0.0765788155284,0.0771212282591,0.0778608819828,0.0770226077626,0.0742612338608,0.075099508081,0.0741626133643,0.075099508081,0.0750008875845,0.0744584748537,0.0758884720529,0.075099508081,0.0742119236125,0.074902267088,0.0759377823012,0.0765295052801,0.0769239872661,0.0772198487556,0.0785512254583,0.0788470869478,0.0783046742171,0.07850191521,0.0780581229758,0.0763815745354,0.0773677795003,0.0779595024793,0.0779101922311,0.0774663999968,0.0759870925494,0.075099508081,0.074705026095,0.0748036465915,0.0748036465915,0.0754939900669,0.0746557158467,0.0732257186476,0.0739653723713,0.0725353751721,0.0720915829379,0.0722888239309,0.0719929624414,0.0717957214484,0.0717464112001,0.0721408931861,0.0720915829379,0.0720915829379,0.0727326161651,0.0748529568397,0.0751981285775,0.0754939900669,0.0763322642872,0.0763322642872,0.0758391618047,0.0767760565214,0.0765295052801,0.0764801950319,0.074902267088,0.074113303116,0.073916062123,0.0733736493923,0.0734722698888,0.0727326161651,0.0736202006335,0.0726339956686,0.0734229596405,0.0728312366616,0.07371882113,0.0721902034344,0.0714998599589,0.0730777879028,0.0732257186476,0.0748529568397,0.0757898515564,0.0759870925494,0.0757405413082,0.0772691590039,0.0767267462731,0.0780581229758,0.0784032947135,0.0773677795003,0.0772691590039,0.0765295052801,0.0765295052801,0.0776636409898,0.0775157102451,0.0773184692521,0.078699156203,0.080079843154,0.0804250148917,0.0809181173742,0.0811646686154,0.0813619096084,0.0814112198566,0.0802277738987,0.0815591506014,0.0800305329057,0.0807701866294,0.0804250148917,0.0813619096084,0.0814605301049,0.0804250148917,0.0816577710979,0.0816084608496,0.0810660481189,0.0800305329057,0.0820522530839,0.0792415689338,0.0783046742171,0.0784526049618,0.0781567434723,0.079093638189,0.0768746770179,0.0760857130459,0.0767267462731,0.0763322642872,0.0766281257766,0.0769239872661,0.0774170897486,0.0770719180109,0.0781567434723,0.0781567434723,0.0778608819828,0.0780581229758,0.0787484664513,0.0789950176925,0.0801291534022,0.0811153583672,0.0804743251399,0.0803263943952,0.0800305329057,0.0814605301049,0.084468455248,0.0845177654962,0.0862436241849,0.0899418928035,0.0901884440447,0.0925060257123,0.0945277458905,0.0960563635862,0.0987684272398,0.098423255502,0.0982753247573,0.100395665432,0.0989163579845,0.0969932583029,0.0987684272398,0.100198424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m <- 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ycorr <- 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altd  <- c(41, 239, 288)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('BW42_mre11_k562_vegfa_xl_16h.2x36mers.hg38-male.unique.MACS-2.1.0_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) : 41,239,288',bty='n')
dev.off()