# R script for Peak Model
#  -- generated by MACS
p <- c(0.0343117021896,0.0401991344841,0.0456012228978,0.0516363685474,0.0575871065655,0.0574815970262,0.0569540493295,0.0567008264351,0.0567852340666,0.0566797245273,0.0569540493295,0.0568485397902,0.0572072722239,0.0569329474216,0.0565953168958,0.0568907436059,0.0572072722239,0.0577770237363,0.0581779599857,0.0582201638014,0.0579669409071,0.0578403294599,0.0580724504464,0.0581990618936,0.0579247370913,0.0575660046576,0.0579669409071,0.0576082084733,0.0572916798554,0.0572283741318,0.0572494760396,0.0574182913026,0.0572283741318,0.0569962531452,0.057354985579,0.0573760874868,0.0570595588688,0.056869641698,0.0567641321587,0.0568063359744,0.0567008264351,0.0561732787385,0.0560677691991,0.0563842978171,0.0563842978171,0.0563209920935,0.0558989539362,0.0562576863699,0.0565109092643,0.0567641321587,0.0568063359744,0.0570806607767,0.0569118455138,0.0566797245273,0.0560677691991,0.0562787882778,0.0568485397902,0.0566375207115,0.0565320111722,0.0559622596598,0.0557090367654,0.0554769157789,0.0555613234104,0.055308100516,0.0559200558441,0.055624629134,0.0554980176868,0.0557090367654,0.0559200558441,0.056405399725,0.0566586226194,0.0573127817632,0.0573971893947,0.0579036351835,0.0578403294599,0.0584944886037,0.0583889790644,0.0579036351835,0.0579036351835,0.0580935523543,0.0584733866958,0.0582623676172,0.0585366924194,0.05813575617,0.058452284788,0.0580513485385,0.0583467752486,0.0586422019588,0.0584311828801,0.0587266095902,0.05813575617,0.0580302466307,0.0576715141969,0.0580091447228,0.0572494760396,0.0571439665003,0.0569329474216,0.0573127817632,0.0577770237363,0.0574182913026,0.0577137180127,0.0579880428149,0.058452284788,0.0583467752486,0.058768813406,0.0588743229453,0.0588321191296,0.0585788962352,0.058283469525,0.05813575617,0.0585788962352,0.058452284788,0.0580091447228,0.0581568580779,0.0585577943273,0.0585155905116,0.058452284788,0.0582623676172,0.0583467752486,0.0590220363003,0.0588110172217,0.0589376286689,0.0592963611026,0.0591064439318,0.058916526761,0.0587266095902,0.0591064439318,0.0593174630105,0.0591697496554,0.0586844057745,0.0583256733408,0.0588110172217,0.0583045714329,0.0584733866958,0.0585577943273,0.0593174630105,0.0591275458397,0.0588532210374,0.0587899153138,0.0585155905116,0.058452284788,0.0577770237363,0.0583256733408,0.0583256733408,0.0581146542621,0.0573971893947,0.0574393932104,0.0575238008419,0.0579880428149,0.0582201638014,0.0588743229453,0.0587899153138,0.0586633038666,0.0588321191296,0.0594651763655,0.0600560297858,0.0600771316936,0.0606679851139,0.060330354588,0.0604569660352,0.0604569660352,0.0605202717588,0.0607945965611,0.0605413736667,0.0604569660352,0.0603092526802,0.0602037431408,0.0600349278779,0.0602670488644,0.0599716221543,0.0599294183386,0.06001382597,0.0599927240622,0.0604569660352,0.0600771316936,0.060182641233,0.0607312908375,0.0604147622195,0.0600771316936,0.0602459469566,0.0603092526802,0.0602248450487,0.06001382597,0.0595073801813,0.0595073801813,0.0594440744577,0.0591908515633,0.0593596668262,0.0596128897206,0.0597817049835,0.0594229725498,0.0598028068914,0.0593596668262,0.0597817049835,0.0600982336015,0.0603725584038,0.0603725584038,0.0602670488644,0.0598239087992,0.0597183992599,0.059549583997,0.0596761954442,0.0602881507723,0.0601615393251,0.0602670488644,0.0598450107071,0.0600771316936,0.0598028068914,0.0599505202464,0.06001382597,0.0602670488644,0.0604358641273,0.0608790041925,0.0607945965611,0.0607101889296,0.0609212080083,0.0606679851139,0.061279940442,0.0618285900465,0.0619129976779,0.0622084243881,0.0619974053094,0.0619129976779,0.062060711033,0.0622295262959,0.0624827491903,0.0629680930712,0.0629469911634,0.0625671568218,0.062841481624,0.0627148701768,0.0629891949791,0.0627148701768,0.0625249530061,0.0620818129409,0.0617863862308,0.0611533289948,0.0611744309026,0.0615542652442,0.0614487557049,0.0611322270869,0.0604780679431,0.0603514564959,0.0605202717588,0.0609845137319,0.0611955328105,0.0617230805072,0.0622928320195,0.0622084243881,0.0626515644532,0.0632635197814,0.0640231884645,0.0641497999117,0.0640864941881,0.0639598827409,0.0636222522151,0.0636644560308,0.0632635197814,0.0634534369521,0.06347453886,0.0637699655701,0.0629891949791,0.0631158064263,0.0632213159656,0.0632635197814,0.0641286980038,0.0645929399769,0.0648250609634,0.0649305705027,0.0647617552398,0.064424124714,0.0649094685949,0.0652259972129,0.0652893029365,0.0655636277387,0.0650993857657,0.0646351437926,0.0644452266218,0.064571838069,0.0647617552398,0.0648672647791,0.0652893029365,0.0653315067522,0.0659434620803,0.0664077040533,0.0666609269477,0.06693525175,0.0674416975388,0.0681380604983,0.0682435700377,0.0689399329972,0.0690243406287,0.0699528245748,0.0697207035883,0.069910620759,0.0698895188512,0.0700583341141,0.0702060474692,0.0698051112197,0.0698473150354,0.0691931558916,0.069446378786,0.0688766272736,0.0695307864175,0.0694041749703,0.0701005379298,0.0706702894422,0.0709446142445,0.0713666524018,0.0721263210849,0.0731814164782,0.073687862267,0.0740465947007,0.0742576137794,0.074764059568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m <- 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ycorr <- 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altd  <- c(140)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('11-PIF4-GSE35315/PIF4-ChIP-Seq-GSM865709/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) : 140',bty='n')
dev.off()