# R script for Peak Model
#  -- generated by MACS
p <- c(0.0175802770751,0.0212944201191,0.0245958806027,0.0287227062072,0.0321892397149,0.0316114841303,0.0317765571545,0.0324368492512,0.0329320683237,0.0330146048358,0.0327669952995,0.0317765571545,0.0311988015698,0.0307861190094,0.0309511920336,0.0310337285457,0.0295480713281,0.0302083634248,0.0307035824973,0.0302083634248,0.0308686555215,0.0310337285457,0.0315289476182,0.0317765571545,0.0311162650578,0.0314464111061,0.0326019222754,0.0321067032028,0.0316114841303,0.0323543127391,0.0314464111061,0.0318590936666,0.0319416301787,0.0311162650578,0.0315289476182,0.0326019222754,0.0334272873963,0.0342526525172,0.0354081636864,0.0358208462469,0.0362335288073,0.0355732367106,0.0360684557831,0.0373890399766,0.0376366495128,0.0361509922952,0.0359033827589,0.0345827985655,0.0346653350776,0.034995481126,0.0353256271743,0.0369763574161,0.0369763574161,0.0363160653194,0.0362335288073,0.0374715764886,0.0378842590491,0.0380493320733,0.0376366495128,0.0372239669524,0.0382969416095,0.037801722537,0.0370588939282,0.0369763574161,0.0379667955612,0.037801722537,0.0382144050975,0.0382144050975,0.03870962417,0.03870962417,0.0380493320733,0.0392873797546,0.0404428909239,0.0403603544118,0.0389572337063,0.0387921606821,0.0386270876579,0.0400302083634,0.0393699162667,0.0397000623151,0.0397000623151,0.0384620146337,0.0378842590491,0.0380493320733,0.03870962417,0.0392873797546,0.03870962417,0.0388746971942,0.0389572337063,0.0395349892909,0.0397000623151,0.0387921606821,0.0384620146337,0.0390397702184,0.0385445511458,0.0382144050975,0.0387921606821,0.0378842590491,0.0386270876579,0.0381318685854,0.0392048432425,0.0416809386052,0.0425063037261,0.0419285481415,0.0431665958228,0.0430015227986,0.0434967418712,0.0448173260646,0.0447347895525,0.0437443514075,0.0430840593107,0.0421761576778,0.0425888402382,0.0425063037261,0.0420936211657,0.0425888402382,0.0421761576778,0.040525427436,0.0403603544118,0.0414333290689,0.0415984020931,0.0412682560448,0.041515865581,0.0423412307019,0.0427539132624,0.0430840593107,0.0430015227986,0.0446522530404,0.0448173260646,0.0454776181613,0.0454776181613,0.0454776181613,0.0453125451372,0.0458903007218,0.0461379102581,0.0454776181613,0.0463029832822,0.0457252276976,0.0469632753789,0.0467982023548,0.047953713524,0.0486965421328,0.0496869802779,0.0501821993504,0.0499345898142,0.0505123453988,0.0493568342295,0.0505123453988,0.0500996628383,0.0510075644713,0.0494393707416,0.0505123453988,0.0507599549351,0.0501821993504,0.0502647358625,0.0511726374955,0.0524106851769,0.0524932216889,0.0527408312252,0.0529059042494,0.0538138058824,0.0534011233219,0.0535661963461,0.0538138058824,0.0539788789066,0.0533185868098,0.0535661963461,0.0524106851769,0.0524932216889,0.0527408312252,0.0538963423945,0.0538963423945,0.0534011233219,0.052575758201,0.0536487328582,0.0546391710033,0.054391561467,0.054391561467,0.0552169265879,0.053483659834,0.0529884407615,0.0539788789066,0.0546391710033,0.0563724377572,0.0567025838055,0.0573628759022,0.0576930219506,0.0595088252166,0.0592612156803,0.0612420919704,0.0610770189463,0.0597564347528,0.0587659966077,0.0580231679989,0.0578580949748,0.0576930219506,0.0583533140473,0.0582707775352,0.0578580949748,0.0565375107813,0.0575279489264,0.0592612156803,0.0616547745309,0.0624801396518,0.062645212676,0.062645212676,0.0620674570913,0.0618198475551,0.0631404317485,0.0650387715266,0.065451454087,0.0656990636233,0.0650387715266,0.0649562350145,0.0652863810628,0.0653689175749,0.0666895017683,0.0671021843288,0.0666895017683,0.0671021843288,0.0661942826958,0.0656990636233,0.065451454087,0.0649562350145,0.0637181873331,0.0629753587243,0.061737311043,0.0611595554583,0.06082940941,0.0594262887045,0.0597564347528,0.0597564347528,0.0602516538254,0.0623976031397,0.0631404317485,0.0635531143089,0.064543552454,0.067267257353,0.0680100859618,0.0699084257398,0.0714766194695,0.0716416924937,0.07188930203,0.0713940829574,0.0735400322718,0.0752732990257,0.0751082260015,0.0723845211025,0.0733749592476,0.07188930203,0.0713940829574,0.0725495941267,0.0725495941267,0.0729622766871,0.0729622766871,0.0735400322718,0.0735400322718,0.075603445074,0.0754383720498,0.0770065657795,0.0758510546103,0.0750256894894,0.0747780799531,0.0748606164652,0.074695543441,0.0753558355377,0.0761812006586,0.0751082260015,0.0763462736828,0.0768414927554,0.0775843213642,0.07741924834,0.0773367118279,0.0771716388037,0.0760986641466,0.0755209085619,0.0764288101949,0.0765938832191,0.075603445074,0.074695543441,0.0751082260015,0.0759335911224,0.0760161276345,0.0761812006586,0.0757685180982,0.0751907625136,0.075603445074,0.0768414927554,0.0758510546103,0.076511346707,0.0777493943883,0.0791525150939,0.0816286104566,0.0818762199928,0.0836920232588,0.0845999248918,0.0835269502346,0.0831142676742,0.0861681186215,0.0867458742061,0.0881489949116,0.0887267504963,0.0885616774721,0.0890568965446,0.0904600172501,0.0917806014436,0.0942566968062,0.0954122079755,0.0941741602942,0.0950820619271,0.0933487951733,0.093101185637,0.0932662586612,0.0930186491249,0.091780601443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m <- 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ycorr <- 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altd  <- c(122)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('RGT1_rep2-GSM5884466.2x25mers.Spar+sacCer3.unique.dedup.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) : 122',bty='n')
dev.off()