# R script for Peak Model
#  -- generated by MACS
p <- c(0.0490730158165,0.0569552100668,0.0642017434905,0.0717025412449,0.0800932641565,0.0820002466364,0.0809831893138,0.0813645858098,0.0802203963218,0.0792033389992,0.0775506208499,0.0770420921886,0.0758979027007,0.0758979027007,0.0747537132127,0.0711940125835,0.0692870301036,0.0695412944343,0.0701769552609,0.0705583517569,0.0708126160876,0.0723382020715,0.0714482769142,0.0696684265996,0.0697955587649,0.0711940125835,0.0727195985675,0.0722110699062,0.0723382020715,0.0709397482529,0.0703040874262,0.0687785014423,0.0704312195916,0.0718296734102,0.0715754090795,0.0714482769142,0.0725924664021,0.0708126160876,0.0697955587649,0.0705583517569,0.0733552593941,0.0722110699062,0.0706854839222,0.0706854839222,0.0710668804182,0.0714482769142,0.0719568055755,0.0720839377408,0.0718296734102,0.0720839377408,0.0692870301036,0.0705583517569,0.0733552593941,0.0731009950635,0.0739909202208,0.0743723167167,0.0723382020715,0.0725924664021,0.0734823915594,0.0727195985675,0.0731009950635,0.0731009950635,0.0718296734102,0.0723382020715,0.0709397482529,0.0708126160876,0.0723382020715,0.0727195985675,0.0723382020715,0.0727195985675,0.0727195985675,0.0724653342368,0.0723382020715,0.0719568055755,0.0724653342368,0.0704312195916,0.069414162269,0.0700498230956,0.0699226909303,0.068651369277,0.069032765773,0.069414162269,0.069414162269,0.0687785014423,0.0680157084503,0.0695412944343,0.0720839377408,0.0719568055755,0.0717025412449,0.0728467307328,0.0728467307328,0.0729738628981,0.0738637880554,0.0743723167167,0.075262241874,0.07564363837,0.0742451845514,0.0736095237248,0.0733552593941,0.0739909202208,0.0736095237248,0.0733552593941,0.0755165062047,0.076025034866,0.0757707705353,0.07564363837,0.0747537132127,0.076406431362,0.0788219425032,0.0786948103379,0.0785676781726,0.0785676781726,0.0770420921886,0.0766606956926,0.0776777530153,0.0774234886846,0.0780591495112,0.0779320173459,0.0771692243539,0.0771692243539,0.0783134138419,0.0800932641565,0.0798389998258,0.0807289249831,0.0813645858098,0.0813645858098,0.0808560571485,0.0795847354952,0.0804746606525,0.0808560571485,0.0795847354952,0.0772963565193,0.0771692243539,0.0757707705353,0.0743723167167,0.074880845378,0.075262241874,0.0755165062047,0.0731009950635,0.0715754090795,0.0724653342368,0.0722110699062,0.0714482769142,0.0727195985675,0.0727195985675,0.0713211447489,0.0706854839222,0.0692870301036,0.068269972781,0.0676343119544,0.0681428406157,0.0681428406157,0.0687785014423,0.0680157084503,0.0667443867971,0.0667443867971,0.0673800476237,0.0687785014423,0.0699226909303,0.0703040874262,0.0689056336076,0.0705583517569,0.0697955587649,0.0709397482529,0.0732281272288,0.0739909202208,0.0751351097087,0.0766606956926,0.0778048851806,0.0813645858098,0.0844157577776,0.0835258326203,0.083398700455,0.0828901717937,0.0823816431324,0.0814917179751,0.0789490746685,0.0772963565193,0.0772963565193,0.0742451845514,0.0720839377408,0.0710668804182,0.0711940125835,0.0705583517569,0.0713211447489,0.0719568055755,0.0732281272288,0.0733552593941,0.0728467307328,0.0736095237248,0.0725924664021,0.0738637880554,0.0724653342368,0.0733552593941,0.0709397482529,0.0705583517569,0.0703040874262,0.0703040874262,0.0713211447489,0.0714482769142,0.0733552593941,0.0728467307328,0.074880845378,0.0741180523861,0.0743723167167,0.0744994488821,0.0739909202208,0.0738637880554,0.0732281272288,0.0720839377408,0.0715754090795,0.0714482769142,0.0717025412449,0.0731009950635,0.0753893740394,0.0743723167167,0.0739909202208,0.0731009950635,0.0720839377408,0.0732281272288,0.0724653342368,0.0720839377408,0.0711940125835,0.0717025412449,0.069414162269,0.0700498230956,0.0704312195916,0.0715754090795,0.0729738628981,0.0736095237248,0.0733552593941,0.0742451845514,0.0746265810474,0.0731009950635,0.076406431362,0.0769149600233,0.0771692243539,0.0783134138419,0.0762792991967,0.0746265810474,0.0755165062047,0.0753893740394,0.0755165062047,0.075262241874,0.0727195985675,0.0733552593941,0.0731009950635,0.0731009950635,0.0753893740394,0.076787827858,0.0778048851806,0.0770420921886,0.0775506208499,0.0788219425032,0.0797118676605,0.0807289249831,0.0812374536444,0.0799661319912,0.0800932641565,0.0792033389992,0.0797118676605,0.0808560571485,0.0802203963218,0.0789490746685,0.0780591495112,0.0772963565193,0.0789490746685,0.0798389998258,0.0779320173459,0.0781862816766,0.0762792991967,0.0779320173459,0.0792033389992,0.0803475284871,0.0812374536444,0.0803475284871,0.0799661319912,0.0793304711645,0.0811103214791,0.0809831893138,0.0803475284871,0.0776777530153,0.0774234886846,0.076025034866,0.0751351097087,0.076406431362,0.0757707705353,0.0757707705353,0.0771692243539,0.0766606956926,0.0783134138419,0.0806017928178,0.0803475284871,0.0809831893138,0.0804746606525,0.0792033389992,0.0781862816766,0.0780591495112,0.0761521670313,0.076025034866,0.07564363837,0.0728467307328,0.0729738628981,0.0739909202208,0.0761521670313,0.0772963565193,0.0783134138419,0.0792033389992,0.0780591495112,0.0799661319912,0.0802203963218,0.083017303959,0.082635907463,0.0835258326203,0.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m <- 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ycorr <- 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altd  <- c(41, 99, 488, 558)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('106-PLT-GSE79755/PLT2_IP2-GSM2102043/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) : 41,99,488,558',bty='n')
dev.off()