# R script for Peak Model
#  -- generated by MACS
p <- c(0.0478807065679,0.0555851269337,0.0640146692164,0.0720589904807,0.0801033117451,0.0795821303674,0.0797407507867,0.0795141501877,0.0797180907268,0.0797180907268,0.0796954306669,0.0800579916253,0.0799446913258,0.0798087309664,0.0800806516852,0.080579173003,0.0804205525837,0.0801712919248,0.0797860709065,0.079899371206,0.0801486318649,0.0803752324639,0.0801486318649,0.0803978925238,0.0800353315654,0.0802619321644,0.0806244931228,0.080579173003,0.080579173003,0.080352572404,0.0806698132426,0.0807377934223,0.0806018330629,0.0803752324639,0.0804432126436,0.080352572404,0.0804205525837,0.0809870540812,0.0813269549797,0.0819161165371,0.0814402552792,0.0809870540812,0.0811230144406,0.0814402552792,0.0816895159381,0.081485575399,0.0818028162376,0.0815762156386,0.0817801561777,0.0814402552792,0.0819840967168,0.0825052780945,0.0825052780945,0.0825505982143,0.0823013375554,0.0822560174356,0.0821427171361,0.0823239976153,0.0818028162376,0.0815762156386,0.0810776943208,0.0811230144406,0.0809870540812,0.081032374201,0.0812589748,0.0813269549797,0.0813949351594,0.0816215357584,0.0821427171361,0.0829584792924,0.0834796606701,0.0837969015087,0.0843407429463,0.0844313831859,0.0845446834854,0.0845673435453,0.0846579837849,0.0847939441443,0.0852018252225,0.0848166042042,0.0847033039047,0.0842047825869,0.0839102018082,0.0839102018082,0.0836609411493,0.0839781819879,0.0835703009097,0.083275720131,0.083049119532,0.0827771988132,0.0827545387533,0.0832530600711,0.0831850798914,0.083049119532,0.0832077399513,0.0831850798914,0.083275720131,0.0831397597716,0.083049119532,0.0831397597716,0.0832530600711,0.0825959183341,0.082822518933,0.0827771988132,0.0830037994122,0.0835249807899,0.0836156210295,0.0840235021077,0.0842274426468,0.084408723126,0.0842501027067,0.0850205447433,0.0850205447433,0.0853377855819,0.0855870462408,0.0854284258215,0.0858136468398,0.0860402474388,0.0857909867799,0.0855190660611,0.085541726121,0.0846579837849,0.084861924324,0.0847259639646,0.0847033039047,0.0843180828864,0.0845673435453,0.0846126636651,0.0847939441443,0.0851791651626,0.0853604456418,0.0859496071992,0.0860402474388,0.085994927319,0.0861308876784,0.0865387687566,0.086448128517,0.0863121681576,0.086674729116,0.0865161086967,0.0863801483373,0.0868786696551,0.0866520690561,0.0873771909729,0.0876264516318,0.0872638906734,0.0872412306135,0.0871959104937,0.0868560095952,0.0870826101942,0.0874678312125,0.0870372900744,0.0878303921709,0.0873318708531,0.0864707885769,0.0862895080977,0.086221527918,0.0861082276185,0.0861082276185,0.0860402474388,0.0856323663606,0.0854284258215,0.0846579837849,0.0851338450428,0.08576832672,0.0866973891759,0.086901329715,0.0872638906734,0.0875358113922,0.0880116726501,0.0881702930694,0.0885101939678,0.0892579759445,0.0890313753455,0.0887594546267,0.0888954149861,0.0888727549262,0.0889407351059,0.0891899957648,0.0887367945668,0.0890087152856,0.0890313753455,0.0889860552257,0.0888727549262,0.0892353158846,0.0888274348064,0.0887141345069,0.0885555140876,0.0887367945668,0.0893032960643,0.0893259561242,0.0892806360044,0.0895298966633,0.0897338372024,0.0901643783405,0.0905495993588,0.0908668401974,0.0912747212756,0.0912520612157,0.0910707807365,0.0913427014553,0.0918412227731,0.0910254606167,0.0912973813355,0.0907761999578,0.0899604378014,0.089597876843,0.0893032960643,0.0889407351059,0.0889407351059,0.088691474447,0.0884422137881,0.0887821146866,0.0883968936683,0.0886688143871,0.0894392564237,0.0900963981608,0.0902550185801,0.0901870384004,0.0900057579212,0.0901190582207,0.0903229987598,0.0904136389994,0.0903683188796,0.0904136389994,0.0904136389994,0.0904816191791,0.0907082197781,0.090957480437,0.0914560017548,0.0916599422939,0.0919092029528,0.0921584636117,0.0927249651092,0.0926116648097,0.0925210245701,0.0924077242706,0.0923397440909,0.0924303843305,0.0925890047498,0.0927249651092,0.093223486427,0.0935180672057,0.0936087074453,0.0938806281641,0.094107228763,0.0943111693021,0.0946963903204,0.0946737302605,0.0947643705001,0.0946284101407,0.094333829362,0.0944924497813,0.0944471296615,0.0945151098412,0.0944244696016,0.0943564894219,0.0941298888229,0.0943791494818,0.0944697897214,0.0951722515783,0.0949456509793,0.0946737302605,0.0946963903204,0.0950816113387,0.0955121524768,0.095466832357,0.0955574725966,0.0953082119377,0.0951949116382,0.0942205290625,0.0937673278646,0.0934954071458,0.093223486427,0.0926796449894,0.0926343248696,0.0924303843305,0.0922037837315,0.0921358035518,0.0922717639112,0.0928156053488,0.0933821068463,0.0936993476849,0.0940165885235,0.0942658491823,0.0939712684037,0.0941752089427,0.094333829362,0.0946963903204,0.0945830900209,0.0947643705001,0.0949003308595,0.0946963903204,0.0944471296615,0.0945377699011,0.0949909710991,0.0948323506798,0.0951042713986,0.0946284101407,0.0947643705001,0.0945830900209,0.0946963903204,0.0948776707996,0.0956254527763,0.0954894924169,0.0949229909194,0.0953308719976,0.0952855518778,0.0962372743936,0.0963052545733,0.0962372743936,0.0961692942139,0.0964638749926,0.0961239740941,0.09669047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m <- 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ycorr <- 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altd  <- c(4, 422, 441)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Pc-C-BioTAP_IP_S2_replicate1-GSM1616476.36mers.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) : 4,422,441',bty='n')
dev.off()