# R script for Peak Model
#  -- generated by MACS
p <- c(0.0423819347879,0.0513136648465,0.0584940752857,0.0647988259153,0.0728548961643,0.0740808198978,0.0742559518597,0.0721543683165,0.0695273888875,0.0684765971159,0.0690019930017,0.0661998816108,0.0651490898392,0.0674258053443,0.0653242218011,0.0647988259153,0.0647988259153,0.0651490898392,0.0669004094585,0.0679512012301,0.0677760692682,0.0672506733824,0.0676009373063,0.0658496176869,0.0679512012301,0.0691771249637,0.0681263331921,0.0695273888875,0.0704030486972,0.0719792363546,0.0725046322404,0.0728548961643,0.0719792363546,0.0726797642023,0.070928444583,0.0688268610398,0.0686517290779,0.0676009373063,0.0670755414205,0.0658496176869,0.0647988259153,0.0654993537631,0.0665501455347,0.0639231661057,0.0644485619915,0.0628723743341,0.0644485619915,0.0646236939534,0.0628723743341,0.0639231661057,0.0642734300295,0.0646236939534,0.0642734300295,0.0646236939534,0.0646236939534,0.0674258053443,0.068301465154,0.0684765971159,0.0698776528114,0.068301465154,0.0695273888875,0.0693522569256,0.0681263331921,0.0681263331921,0.0674258053443,0.065674485725,0.0616464506005,0.0607707907909,0.0605956588289,0.0595448670573,0.0567427556664,0.0565676237045,0.057793547438,0.0588443392096,0.0602453949051,0.0609459227528,0.063047506296,0.0628723743341,0.0637480341437,0.0651490898392,0.0658496176869,0.0651490898392,0.0651490898392,0.0644485619915,0.0644485619915,0.065674485725,0.0651490898392,0.0669004094585,0.0658496176869,0.0647988259153,0.0663750135727,0.0681263331921,0.068301465154,0.0684765971159,0.0669004094585,0.0669004094585,0.0669004094585,0.0644485619915,0.0660247496489,0.0660247496489,0.0646236939534,0.0647988259153,0.0639231661057,0.0646236939534,0.0635729021818,0.0612961866767,0.0607707907909,0.0618215825625,0.0591946031335,0.0597199990193,0.060420526867,0.0602453949051,0.0590194711715,0.0572681515522,0.0579686793999,0.0602453949051,0.0618215825625,0.0602453949051,0.0602453949051,0.060420526867,0.0588443392096,0.0581438113619,0.0600702629431,0.0605956588289,0.0609459227528,0.0597199990193,0.0579686793999,0.0619967145244,0.0602453949051,0.0588443392096,0.0611210547147,0.0618215825625,0.0633977702199,0.0654993537631,0.068301465154,0.0679512012301,0.0704030486972,0.0691771249637,0.0704030486972,0.0716289724307,0.0702279167353,0.0695273888875,0.0686517290779,0.0663750135727,0.0644485619915,0.0637480341437,0.063047506296,0.0623469784483,0.063047506296,0.0635729021818,0.0635729021818,0.063047506296,0.0625221104102,0.0635729021818,0.0623469784483,0.0637480341437,0.0640982980676,0.0654993537631,0.0667252774966,0.0654993537631,0.0658496176869,0.0658496176869,0.065674485725,0.0670755414205,0.0690019930017,0.0679512012301,0.0676009373063,0.0670755414205,0.0674258053443,0.0698776528114,0.070928444583,0.0716289724307,0.0702279167353,0.0704030486972,0.068301465154,0.0690019930017,0.0684765971159,0.0676009373063,0.0674258053443,0.0646236939534,0.0653242218011,0.0649739578773,0.0676009373063,0.0669004094585,0.0663750135727,0.0676009373063,0.0669004094585,0.0658496176869,0.0635729021818,0.0646236939534,0.0632226382579,0.0642734300295,0.0642734300295,0.0632226382579,0.0665501455347,0.0661998816108,0.0686517290779,0.0707533126211,0.0749564797075,0.0749564797075,0.073555424012,0.0728548961643,0.0740808198978,0.0749564797075,0.0749564797075,0.0742559518597,0.0728548961643,0.0719792363546,0.0704030486972,0.0716289724307,0.0733802920501,0.073555424012,0.0712787085069,0.0725046322404,0.0725046322404,0.0732051600881,0.0740808198978,0.0746062157836,0.0726797642023,0.0707533126211,0.070928444583,0.0704030486972,0.0707533126211,0.068301465154,0.068301465154,0.0679512012301,0.0681263331921,0.0697025208495,0.0725046322404,0.0723295002785,0.0711035765449,0.0721543683165,0.0732051600881,0.0742559518597,0.0739056879359,0.0753067436313,0.0739056879359,0.0719792363546,0.0702279167353,0.0714538404688,0.0712787085069,0.0702279167353,0.0693522569256,0.0704030486972,0.0695273888875,0.0686517290779,0.0698776528114,0.0705781806591,0.0693522569256,0.0707533126211,0.0702279167353,0.0716289724307,0.0718041043927,0.0705781806591,0.0707533126211,0.0716289724307,0.0719792363546,0.0712787085069,0.0732051600881,0.0719792363546,0.0746062157836,0.0732051600881,0.0746062157836,0.0774083271745,0.0779337230603,0.0756570075552,0.0744310838217,0.0763575354029,0.0767077993268,0.076182403441,0.0751316116694,0.0768829312887,0.0740808198978,0.0725046322404,0.0702279167353,0.0714538404688,0.0716289724307,0.0705781806591,0.0697025208495,0.0711035765449,0.070928444583,0.0686517290779,0.0704030486972,0.0691771249637,0.0714538404688,0.0718041043927,0.0725046322404,0.0723295002785,0.0747813477455,0.0739056879359,0.0747813477455,0.0756570075552,0.0758321395171,0.0782839869842,0.0774083271745,0.0781088550223,0.0795099107177,0.0779337230603,0.0779337230603,0.0809109664132,0.0807358344513,0.0824871540706,0.0816114942609,0.0826622860325,0.0837130778041,0.0847638695757,0.084063341728,0.0887919047002,0.0889670366621,0.0863400572331,0.0886167727383,0.0859897933093,0.0896675645099,0.089317300586,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m <- 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ycorr <- 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altd  <- c(42, 65, 528, 561)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('16-TOC1-GSE35952/TOC1_ChIPSeq-GSM878068/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) : 42,65,528,561',bty='n')
dev.off()