# R script for Peak Model
#  -- generated by MACS
p <- c(0.018619098654,0.0217979691559,0.0249768396578,0.0299722075893,0.0363299485931,0.0381464460228,0.0376923216654,0.0417794408821,0.0408711921673,0.0404170678098,0.0422335652395,0.0426876895969,0.0440500626692,0.0431418139543,0.039508819095,0.0363299485931,0.0381464460228,0.0340593268061,0.0336052024486,0.0363299485931,0.0354216998783,0.0358758242357,0.0340593268061,0.0326969537338,0.0336052024486,0.0376923216654,0.0367840729505,0.0386005703802,0.0417794408821,0.039508819095,0.0413253165247,0.0413253165247,0.0417794408821,0.0426876895969,0.0417794408821,0.037238197308,0.0349675755209,0.0336052024486,0.0322428293764,0.0340593268061,0.0340593268061,0.0354216998783,0.037238197308,0.0386005703802,0.0390546947376,0.0426876895969,0.0463206844562,0.0485913062433,0.0476830575285,0.0458665600988,0.044958311384,0.0431418139543,0.0413253165247,0.0404170678098,0.0417794408821,0.0386005703802,0.0376923216654,0.0376923216654,0.0386005703802,0.0404170678098,0.0390546947376,0.0390546947376,0.037238197308,0.0376923216654,0.0376923216654,0.0390546947376,0.0376923216654,0.0363299485931,0.0381464460228,0.0354216998783,0.0376923216654,0.0408711921673,0.0426876895969,0.0440500626692,0.0454124357414,0.0463206844562,0.0494995549581,0.0499536793155,0.0494995549581,0.0513160523878,0.0517701767452,0.0490454306007,0.0494995549581,0.0494995549581,0.0490454306007,0.0508619280304,0.0499536793155,0.0508619280304,0.0513160523878,0.0508619280304,0.0499536793155,0.0494995549581,0.0499536793155,0.0485913062433,0.0481371818859,0.0458665600988,0.0435959383117,0.044958311384,0.0422335652395,0.0408711921673,0.0417794408821,0.0440500626692,0.0426876895969,0.0422335652395,0.0399629434524,0.039508819095,0.039508819095,0.037238197308,0.0386005703802,0.0408711921673,0.0408711921673,0.0413253165247,0.0435959383117,0.044958311384,0.0467748088136,0.0458665600988,0.0481371818859,0.0494995549581,0.0508619280304,0.0485913062433,0.0476830575285,0.0445041870266,0.0426876895969,0.0404170678098,0.0399629434524,0.0426876895969,0.0408711921673,0.0404170678098,0.0390546947376,0.0408711921673,0.0413253165247,0.0426876895969,0.0431418139543,0.0431418139543,0.0445041870266,0.0426876895969,0.0435959383117,0.0431418139543,0.0431418139543,0.0426876895969,0.0417794408821,0.0417794408821,0.0440500626692,0.0435959383117,0.0422335652395,0.0422335652395,0.0422335652395,0.0408711921673,0.0399629434524,0.0404170678098,0.0426876895969,0.0422335652395,0.0413253165247,0.0426876895969,0.044958311384,0.0481371818859,0.0472289331711,0.0476830575285,0.0490454306007,0.0481371818859,0.0454124357414,0.0458665600988,0.0472289331711,0.0467748088136,0.0431418139543,0.0408711921673,0.0426876895969,0.0445041870266,0.0458665600988,0.0472289331711,0.0485913062433,0.0490454306007,0.0485913062433,0.0476830575285,0.0485913062433,0.0476830575285,0.0445041870266,0.044958311384,0.0408711921673,0.0386005703802,0.0390546947376,0.0399629434524,0.0413253165247,0.0445041870266,0.0472289331711,0.0508619280304,0.0531325498174,0.0535866741749,0.0544949228897,0.0558572959619,0.0567655446768,0.0544949228897,0.0522243011026,0.0517701767452,0.0494995549581,0.0476830575285,0.0467748088136,0.044958311384,0.0467748088136,0.0490454306007,0.0485913062433,0.0508619280304,0.0490454306007,0.0494995549581,0.0517701767452,0.0540407985323,0.0590361664638,0.0603985395361,0.0599444151787,0.0576737933916,0.0549490472471,0.0544949228897,0.0563114203193,0.0535866741749,0.0540407985323,0.0513160523878,0.0467748088136,0.0454124357414,0.0458665600988,0.0476830575285,0.0481371818859,0.0467748088136,0.0490454306007,0.0490454306007,0.0476830575285,0.0476830575285,0.0513160523878,0.050407803673,0.0481371818859,0.0458665600988,0.0481371818859,0.0490454306007,0.0494995549581,0.0531325498174,0.0567655446768,0.0572196690342,0.0549490472471,0.0572196690342,0.0617609126083,0.0631232856806,0.0640315343954,0.0640315343954,0.0640315343954,0.0613067882509,0.0567655446768,0.0558572959619,0.0558572959619,0.0535866741749,0.0513160523878,0.0535866741749,0.0531325498174,0.0549490472471,0.0522243011026,0.0576737933916,0.0585820421064,0.0608526638935,0.0613067882509,0.0626691613231,0.0622150369657,0.0594902908212,0.0603985395361,0.0585820421064,0.0599444151787,0.0563114203193,0.0549490472471,0.05267842546,0.050407803673,0.050407803673,0.0563114203193,0.0594902908212,0.0585820421064,0.0613067882509,0.0590361664638,0.0599444151787,0.0603985395361,0.0644856587528,0.0681186536121,0.0685727779695,0.0644856587528,0.0613067882509,0.0622150369657,0.0603985395361,0.0622150369657,0.0644856587528,0.0663021561824,0.0649397831102,0.0653939074676,0.0703892753992,0.0690269023269,0.0699351510418,0.0690269023269,0.0676645292547,0.0703892753992,0.0676645292547,0.0672104048973,0.0631232856806,0.0599444151787,0.0563114203193,0.0572196690342,0.058127917749,0.0608526638935,0.0603985395361,0.0594902908212,0.0622150369657,0.0672104048973,0.0717516484714,0.0717516484714,0.0717516484714,0.0749305189733,0.076747016403,0.0758387676881,0.07901763819,0.0808341356197,0.083104757406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m <- 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ycorr <- 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altd  <- c(111)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('hyb_cswi5_rep2-GSM5884480.2x25mers.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) : 111',bty='n')
dev.off()