# R script for Peak Model
#  -- generated by MACS
p <- c(0.0439152715569,0.0508805564073,0.0578458412578,0.0648960686064,0.0717764109586,0.0709269859768,0.0713516984677,0.071011928475,0.0711818134714,0.0717764109586,0.0710968709732,0.0714366409659,0.0713516984677,0.071946295955,0.0716914684604,0.0711818134714,0.0710968709732,0.0714366409659,0.0713516984677,0.0709269859768,0.0714366409659,0.0718613534568,0.072455950944,0.0715215834641,0.0718613534568,0.0718613534568,0.0720312384531,0.0711818134714,0.0711818134714,0.0705872159841,0.0704173309878,0.0699926184969,0.0699076759987,0.0701625034933,0.0717764109586,0.071946295955,0.0727107784385,0.0737300884166,0.0738150309148,0.0747493983948,0.0757687083729,0.0755138808783,0.0755988233765,0.0761934208637,0.0752590533838,0.0759385933692,0.0746644558966,0.0750042258893,0.0750042258893,0.0744096284021,0.0727957209367,0.0733903184239,0.0730505484312,0.0722860659477,0.0717764109586,0.0708420434787,0.0707571009805,0.069567906006,0.069567906006,0.0699076759987,0.0707571009805,0.0700775609951,0.0698227335006,0.0705872159841,0.0716914684604,0.0728806634349,0.0739849159112,0.0750042258893,0.075343995882,0.0750891683875,0.0756837658747,0.0755988233765,0.0761934208637,0.0757687083729,0.0745795133984,0.0744945709002,0.0738150309148,0.0727107784385,0.0709269859768,0.0706721584823,0.0700775609951,0.0704173309878,0.0696528485042,0.069567906006,0.0700775609951,0.0693980210097,0.0698227335006,0.0701625034933,0.0710968709732,0.0713516984677,0.0713516984677,0.0711818134714,0.0716065259622,0.0713516984677,0.0705872159841,0.0704173309878,0.0700775609951,0.0702474459914,0.0704173309878,0.0708420434787,0.0704173309878,0.069567906006,0.0688034235224,0.0688034235224,0.0689733085188,0.069567906006,0.069058251017,0.069058251017,0.0689733085188,0.0678690560425,0.0682088260352,0.0693980210097,0.0701625034933,0.0701625034933,0.0701625034933,0.0691431935151,0.0692281360133,0.0691431935151,0.0698227335006,0.070502273486,0.0701625034933,0.0688883660206,0.0692281360133,0.0699926184969,0.0694829635079,0.0693980210097,0.0688034235224,0.0687184810243,0.0676991710462,0.068123883537,0.0682088260352,0.0693130785115,0.0693130785115,0.0686335385261,0.0702474459914,0.0716914684604,0.0737300884166,0.073899973413,0.075343995882,0.0755138808783,0.0768729608492,0.0773826158382,0.0777223858309,0.0778922708273,0.0778922708273,0.0784019258163,0.07729767334,0.07729767334,0.0777223858309,0.0778922708273,0.0775525008346,0.0769579033473,0.0762783633619,0.0762783633619,0.0757687083729,0.0750042258893,0.0755138808783,0.0755138808783,0.0741548009075,0.0733903184239,0.0729656059331,0.0733053759258,0.0735602034203,0.0742397434057,0.0738150309148,0.0737300884166,0.0735602034203,0.0743246859039,0.0743246859039,0.0740698584093,0.0741548009075,0.0725408934422,0.0716914684604,0.0716065259622,0.0714366409659,0.0711818134714,0.0716914684604,0.0705872159841,0.0700775609951,0.0693980210097,0.069058251017,0.0699076759987,0.0708420434787,0.0703323884896,0.0702474459914,0.0696528485042,0.0687184810243,0.0688034235224,0.0691431935151,0.0696528485042,0.0699926184969,0.0711818134714,0.0711818134714,0.0709269859768,0.071946295955,0.0731354909294,0.0734752609221,0.0732204334276,0.0739849159112,0.0745795133984,0.0737300884166,0.0733903184239,0.0731354909294,0.0744945709002,0.0738150309148,0.0733053759258,0.0741548009075,0.0750891683875,0.0761084783656,0.075853650871,0.0767030758528,0.0770428458455,0.0770428458455,0.0760235358674,0.0763633058601,0.0760235358674,0.0761084783656,0.0768729608492,0.0760235358674,0.075853650871,0.0765331908564,0.0756837658747,0.0757687083729,0.0764482483583,0.0765331908564,0.0772127308419,0.075853650871,0.0750042258893,0.0755988233765,0.0765331908564,0.0759385933692,0.0763633058601,0.0769579033473,0.0770428458455,0.0771277883437,0.07823204082,0.079676063289,0.079676063289,0.0794212357944,0.0792513507981,0.0792513507981,0.079676063289,0.0801007757798,0.0804405457725,0.0806104307689,0.0800158332817,0.0803556032744,0.0806953732671,0.0800158332817,0.0795061782926,0.0795911207908,0.0795061782926,0.0795061782926,0.0801007757798,0.0806104307689,0.0814598557506,0.0813749132525,0.0819695107397,0.0827339932233,0.0846027281832,0.0856220381613,0.0860467506521,0.0865564056412,0.086471463143,0.0868961756339,0.0860467506521,0.0860467506521,0.0858768656558,0.085961808154,0.0846027281832,0.0837533032014,0.0834135332087,0.0829888207178,0.0824791657288,0.0820544532379,0.0823092807324,0.0820544532379,0.0813749132525,0.0810351432598,0.0808652582634,0.0806953732671,0.0812899707543,0.0813749132525,0.0812050282561,0.0809502007616,0.0802706607762,0.0806104307689,0.0824791657288,0.0833285907105,0.085027440674,0.0857069806594,0.0851973256704,0.0857919231576,0.0865564056412,0.0870660606303,0.0881703131065,0.0884251406011,0.0871510031284,0.0874907731211,0.0873208881248,0.087915485612,0.0894444505792,0.0883401981029,0.0888498530919,0.0890197380883,0.0901239905646,0.0902938755609,0.0906336455536,0.0902089330628,0.09080353055,0.0902089330628,0.0899541055682,0.091313185539,0.0901239905646,0.090208933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m <- 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ycorr <- 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altd  <- c(4, 272)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('DAPseq_of_N_crassa_NCU00445_MAN-1.1x36mers.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) : 4,272',bty='n')
dev.off()