# R script for Peak Model
#  -- generated by MACS
p <- c(0.022323227834,0.0261592404898,0.0299783544114,0.0331046202322,0.0369237341538,0.0373293037738,0.0367885442805,0.0368054430147,0.0363491771922,0.035926708838,0.0363998733947,0.0362815822555,0.0362815822555,0.0368561392172,0.0368054430147,0.0369237341538,0.037650379723,0.0376165822547,0.0374644936472,0.0378869620013,0.0377348733938,0.0371265189638,0.0372955063055,0.0372617088372,0.0374982911155,0.0371265189638,0.0369575316222,0.0365857594705,0.0368054430147,0.0369237341538,0.0368223417488,0.0373124050397,0.0367209493438,0.0369744303563,0.0367716455463,0.0367885442805,0.036028101243,0.0367040506097,0.0368730379513,0.0366702531413,0.0364674683313,0.0366533544072,0.0371265189638,0.0371265189638,0.0370251265588,0.0373124050397,0.0374306961788,0.0368899366855,0.0370758227613,0.0371603164322,0.037751772128,0.0381404430138,0.0380052531405,0.0380390506088,0.0379207594697,0.0377179746597,0.0378362657988,0.038157341748,0.0383939240263,0.0386305063047,0.0381404430138,0.0379376582038,0.0379376582038,0.0376672784572,0.0379038607355,0.0377010759255,0.038055949343,0.0385798101022,0.0382080379505,0.0382925316213,0.0385122151655,0.0386136075705,0.0389515822538,0.0391881645322,0.0395937341522,0.0405400632655,0.0404386708605,0.0401006961772,0.0400668987088,0.0404386708605,0.0405400632655,0.040489367063,0.0404386708605,0.040996329088,0.0409287341513,0.0409625316196,0.0412160126321,0.0412836075688,0.0412498101005,0.0416553797205,0.0413512025055,0.0415877847838,0.0415708860496,0.0407428480755,0.0411484176955,0.0409287341513,0.0412329113663,0.041401898708,0.0416215822521,0.0409118354171,0.041199113898,0.0410808227588,0.040996329088,0.0417567721255,0.0410301265563,0.0413343037713,0.041199113898,0.0412836075688,0.0417229746571,0.041706075923,0.0418581645305,0.0421454430113,0.0425003164288,0.042314430353,0.0428889873146,0.0427368987071,0.042719999973,0.0425679113655,0.0419426582013,0.0421623417455,0.0422637341505,0.0418243670621,0.0415201898471,0.0419595569355,0.0421961392138,0.0422468354163,0.0425510126313,0.0429903797196,0.043328354403,0.0430072784538,0.0434128480738,0.0442915822504,0.0453055063004,0.0453562025029,0.0451703164271,0.0454068987054,0.0456772784521,0.0458800632621,0.0459645569329,0.0462856328821,0.0464039240213,0.0460659493379,0.0456265822496,0.0453731012371,0.0457955695913,0.0457786708571,0.0453224050346,0.0451872151613,0.0453224050346,0.0457786708571,0.0458800632621,0.0458800632621,0.0465729113629,0.0470460759196,0.0467925949071,0.0465391138946,0.0470291771854,0.0478572151596,0.0484655695896,0.0480262025012,0.0479586075646,0.0485162657921,0.0479248100963,0.0478234176913,0.0480431012354,0.0483134809821,0.0488204430071,0.0479248100963,0.0480093037671,0.0490570252854,0.0494625949054,0.0493443037662,0.0497836708546,0.0499864556646,0.0494118987029,0.0499864556646,0.0498005695887,0.0505610126262,0.0500878480696,0.0498512657912,0.0495301898421,0.0495470885762,0.0500709493354,0.0507468987021,0.0512876581954,0.0515411392079,0.0521494936379,0.0527916455362,0.053281708827,0.0531634176879,0.0535689873079,0.0538224683204,0.0532479113587,0.0531634176879,0.0542280379404,0.0539407594595,0.0539238607254,0.0531296202195,0.0536534809787,0.0548532911045,0.0548701898387,0.0550898733829,0.0553940505979,0.0552757594587,0.0552757594587,0.0558841138887,0.0562389873062,0.0567628480653,0.057236012622,0.0565431645212,0.0567966455337,0.0572529113562,0.0580640505962,0.0580809493303,0.0580978480645,0.058351329077,0.0581992404695,0.0586386075578,0.0583006328745,0.0588413923678,0.0593821518612,0.0591962657853,0.0593314556587,0.0593821518612,0.0601932911011,0.0605481645186,0.061494493632,0.062204240467,0.0633026581878,0.0636406328711,0.0636744303394,0.0641137974278,0.0646207594528,0.0653136075536,0.0652122151486,0.0655332910978,0.0656346835028,0.0654656961611,0.0644855695794,0.0647390505919,0.0652967088194,0.0658205695786,0.0655839873003,0.0657698733761,0.0665303164136,0.0672231645144,0.0672400632486,0.0676794303369,0.0689130379311,0.0687778480577,0.0695382910952,0.0696903797027,0.0700790505886,0.0712619619802,0.0708901898286,0.0701297467911,0.0701128480569,0.0706874050186,0.071042278436,0.0717351265369,0.071752025271,0.0720224050177,0.0726138607135,0.0722758860302,0.0732898100802,0.0749627847627,0.0761625948885,0.0764498733693,0.0771765189385,0.077328607546,0.0777510759002,0.0782242404568,0.0788156961526,0.0796099366585,0.0797451265318,0.0791874683043,0.0789677847601,0.0785791138743,0.0787987974185,0.0794916455193,0.0799141138735,0.0804210758985,0.0800493037468,0.0804210758985,0.0806576581768,0.0824827214668,0.0836149366559,0.0846626581743,0.0854399999459,0.0862004429834,0.0863525315909,0.0872650632359,0.0884986708301,0.0891577214626,0.0902054429809,0.0895632910826,0.0893098100701,0.0903575315884,0.0903575315884,0.091236265765,0.0920812024734,0.0927064556375,0.0936020885484,0.0941259493075,0.0939907594342,0.0952412657625,0.0969987341158,0.0972860125967,0.097928164495,0.0979450632291,0.0985027214566,0.0986717087983,0.0988068986716,0.0997870252533,0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m <- 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ycorr <- 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altd  <- c(231)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-0.5h-p300.pooled.sorted.MACS-2.1.0.p1e-1_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) : 231',bty='n')
dev.off()