# R script for Peak Model
#  -- generated by MACS
p <- c(0.0445048432645,0.0522297771991,0.0594166560337,0.0666803998826,0.0744821988313,0.0743284688028,0.0741363062671,0.07409787376,0.0742131712814,0.0745590638456,0.0744053338171,0.0740210087457,0.0745974963528,0.0743284688028,0.0734445211386,0.0730986285744,0.0733676561244,0.073252358603,0.0730986285744,0.0725605734745,0.0725221409674,0.0728296010245,0.0726374384888,0.0727527360102,0.0728296010245,0.0728680335316,0.0730986285744,0.0724452759531,0.0718303558389,0.0728680335316,0.0725605734745,0.0720993833889,0.0715613282889,0.071868788346,0.0723299784317,0.0724452759531,0.0718303558389,0.0722915459245,0.0732139260958,0.072406843446,0.072714303503,0.0729448985459,0.0734445211386,0.0735598186601,0.0727911685173,0.0724452759531,0.071868788346,0.0715228957818,0.0714460307675,0.0717919233318,0.0718303558389,0.0719456533603,0.0714460307675,0.0712538682318,0.0714460307675,0.0717534908246,0.0725221409674,0.0729064660387,0.0722531134174,0.0722915459245,0.0722531134174,0.072137815896,0.0722146809103,0.0720225183746,0.0725221409674,0.072983331053,0.0729064660387,0.0727911685173,0.0729448985459,0.0725990059816,0.0722146809103,0.0720609508817,0.0719840858674,0.0725990059816,0.073252358603,0.0725221409674,0.0726374384888,0.0724452759531,0.072714303503,0.0729448985459,0.0735598186601,0.0734829536458,0.0740210087457,0.073252358603,0.072714303503,0.0730601960673,0.0729448985459,0.072983331053,0.0728680335316,0.0733292236172,0.0734829536458,0.0736366836743,0.073252358603,0.0739441437314,0.0733292236172,0.0729064660387,0.0724452759531,0.0729064660387,0.0734445211386,0.0731370610816,0.0724837084602,0.0731754935887,0.0737904137029,0.0736366836743,0.0739057112243,0.0746359288599,0.0755583090312,0.0752124164669,0.0752508489741,0.0752892814812,0.075788904074,0.0745590638456,0.0738672787172,0.0733676561244,0.0735213861529,0.072983331053,0.0723299784317,0.0725605734745,0.0719840858674,0.0723684109388,0.0722146809103,0.0725221409674,0.073252358603,0.07382884621,0.0742900362957,0.0746359288599,0.0741747387742,0.0739057112243,0.0739057112243,0.0742516037885,0.0745974963528,0.0746359288599,0.0742516037885,0.0739825762386,0.0730986285744,0.0735982511672,0.074674361367,0.0744437663242,0.0744821988313,0.07409787376,0.0739825762386,0.0738672787172,0.0737519811957,0.07382884621,0.0742900362957,0.07382884621,0.0740594412528,0.0745206313385,0.074674361367,0.0745206313385,0.0742516037885,0.0749049564099,0.0752892814812,0.0754814440169,0.0763269591739,0.0761732291454,0.0758273365811,0.0762500941596,0.0762116616525,0.0755967415383,0.0757504715669,0.0756736065526,0.0757504715669,0.0758657690883,0.0748280913956,0.0752124164669,0.0752124164669,0.0748665239027,0.0753661464955,0.0761347966382,0.0759426341025,0.0761347966382,0.0756736065526,0.0751355514527,0.0751739839598,0.0753661464955,0.0747512263813,0.0744053338171,0.0745974963528,0.0746359288599,0.0745206313385,0.0744821988313,0.0745206313385,0.0751739839598,0.0756736065526,0.0752124164669,0.0760963641311,0.0767112842453,0.0767881492596,0.0765575542167,0.0769803117952,0.0770571768095,0.0775952319094,0.0765959867239,0.0764038241882,0.0767881492596,0.0765191217096,0.0763653916811,0.0758657690883,0.0764806892025,0.0765191217096,0.0767881492596,0.0768650142738,0.0779795569808,0.0782101520236,0.0784407470664,0.0789403696592,0.0792862622235,0.0793631272377,0.0787097746164,0.0786713421093,0.0787866396307,0.0796705872948,0.0790556671806,0.0793631272377,0.0795937222806,0.0792478297163,0.0794784247591,0.0799780473519,0.0803623724233,0.0806313999733,0.080285507409,0.0792862622235,0.0790556671806,0.0793246947306,0.0793631272377,0.0790556671806,0.0790556671806,0.0785176120807,0.0785560445879,0.0788250721378,0.0787482071235,0.0787482071235,0.0793246947306,0.0793246947306,0.0791325321949,0.0790940996878,0.0786713421093,0.0784023145593,0.0780564219951,0.0776720969237,0.0772493393452,0.0779411244737,0.0779795569808,0.077479934388,0.0772493393452,0.0780564219951,0.0782870170379,0.0786329096021,0.0789788021664,0.0794015597449,0.080285507409,0.0800933448733,0.080554534959,0.0807466974947,0.0818228076945,0.0818612402016,0.082245565273,0.0827836203729,0.0835138380085,0.0833216754728,0.0829757829086,0.0830526479229,0.0828604853872,0.0830142154157,0.082245565273,0.082514592823,0.0820918352445,0.0820918352445,0.0812463200874,0.0814384826231,0.0815153476374,0.0807466974947,0.0807466974947,0.0809004275232,0.081400050116,0.0814769151303,0.0815922126517,0.0807851300018,0.0811694550732,0.0818612402016,0.0826298903444,0.0833216754728,0.0843593531655,0.0845899482084,0.0847436782369,0.0845899482084,0.0846283807155,0.0852048683225,0.0855123283796,0.0849742732797,0.0852048683225,0.0851280033083,0.0849742732797,0.0851664358154,0.084782110744,0.084782110744,0.0853585983511,0.0858582209439,0.0852048683225,0.0855123283796,0.0848974082654,0.0857044909153,0.0855891933939,0.0862425460152,0.0865500060723,0.0865884385795,0.0867806011152,0.0865115735652,0.0872033586937,0.087856711315,0.0882410363864,0.0880873063578,0.0880873063578,0.08762611627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m <- 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ycorr <- 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altd  <- c(3, 208)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('33-SEP3-AP1-24581456/AP1-ChIP-seq-2d-biological-replicate-1-GSM1142626/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) : 3,208',bty='n')
dev.off()