# R script for Peak Model
#  -- generated by MACS
p <- c(0.0451784826993,0.053881868158,0.0621896451867,0.0693897186116,0.0775392522684,0.0782513474423,0.0781722257563,0.0787260775582,0.0779348606984,0.0773018872105,0.0774601305824,0.0784095908143,0.0776974956404,0.0791216859882,0.0789634426162,0.0795172944181,0.0794381727321,0.0795172944181,0.0797546594761,0.080624998022,0.080308511278,0.0792008076742,0.0784095908143,0.0781722257563,0.0780139823843,0.0772227655245,0.0775392522684,0.0768271570945,0.0773810088964,0.0773018872105,0.0781722257563,0.0760359402346,0.0769854004665,0.0764315486646,0.0775392522684,0.0776974956404,0.0761941836066,0.0767480354085,0.0762733052926,0.0751656016888,0.0747699932588,0.0756403318047,0.0751656016888,0.0753238450607,0.0748491149448,0.0754029667467,0.0765897920366,0.0769062787805,0.0767480354085,0.0783304691283,0.0776183739544,0.0778557390124,0.0776183739544,0.0773018872105,0.0767480354085,0.0758776968627,0.0775392522684,0.0765106703506,0.0770645221525,0.0761941836066,0.0764315486646,0.0768271570945,0.0783304691283,0.0780139823843,0.0784095908143,0.0793590510461,0.0773018872105,0.0784887125003,0.0769854004665,0.0776183739544,0.0780931040703,0.0790425643022,0.0784095908143,0.0784887125003,0.0779348606984,0.0776974956404,0.0788843209302,0.0791216859882,0.0799920245341,0.0785678341863,0.0781722257563,0.0762733052926,0.0766689137225,0.0775392522684,0.0778557390124,0.0772227655245,0.0774601305824,0.0770645221525,0.0777766173264,0.0784887125003,0.0791216859882,0.0798337811621,0.0784887125003,0.0784887125003,0.0770645221525,0.0766689137225,0.0764315486646,0.0758776968627,0.0755612101187,0.0765897920366,0.0765897920366,0.0763524269786,0.0772227655245,0.0769062787805,0.0781722257563,0.0794381727321,0.0797546594761,0.080624998022,0.0808623630799,0.0807041197079,0.080308511278,0.0810206064519,0.080624998022,0.08046675465,0.08046675465,0.0818118233118,0.0817327016258,0.0814953365678,0.0818909449978,0.0816535799398,0.0829195269156,0.0834733787175,0.0852931774953,0.0851349341233,0.0846602040074,0.0823656751137,0.0814953365678,0.0827612835436,0.0822865534277,0.0824447967997,0.0829195269156,0.0821283100557,0.0808623630799,0.0817327016258,0.0826821618577,0.0829986486016,0.0846602040074,0.0836316220895,0.0847393256933,0.0854514208672,0.0840272305194,0.0847393256933,0.0838689871475,0.0833151353456,0.0830777702876,0.0826030401717,0.0821283100557,0.0814162148818,0.0799129028481,0.0791216859882,0.0789634426162,0.0788051992442,0.0814953365678,0.0815744582538,0.0819700666838,0.0826030401717,0.0815744582538,0.0808623630799,0.0817327016258,0.0808623630799,0.0795964161041,0.0784887125003,0.0770645221525,0.0773018872105,0.0765106703506,0.0769062787805,0.0769062787805,0.0786469558723,0.0784095908143,0.0789634426162,0.0799129028481,0.08007114622,0.0790425643022,0.0776974956404,0.0782513474423,0.0786469558723,0.0788051992442,0.0785678341863,0.0780139823843,0.0790425643022,0.080308511278,0.080624998022,0.0810997281379,0.0819700666838,0.0819700666838,0.080545876336,0.0810206064519,0.0821283100557,0.0818909449978,0.0825239184857,0.08007114622,0.0795964161041,0.0794381727321,0.0798337811621,0.0792799293602,0.0818909449978,0.0818909449978,0.0810997281379,0.0810206064519,0.080545876336,0.0814162148818,0.0830777702876,0.0826821618577,0.0822865534277,0.0833151353456,0.0816535799398,0.0826821618577,0.0832360136596,0.0842645955774,0.0838689871475,0.0852140558093,0.0848975690653,0.0859261509832,0.0857679076112,0.0845810823214,0.0839481088335,0.0836316220895,0.0819700666838,0.0821283100557,0.0811788498239,0.0813370931959,0.0812579715099,0.0813370931959,0.0822074317417,0.0826030401717,0.0822074317417,0.0825239184857,0.0833942570315,0.0828404052296,0.0836316220895,0.0835525004035,0.0835525004035,0.0831568919736,0.0827612835436,0.0833151353456,0.0841854738914,0.0833151353456,0.0827612835436,0.0822865534277,0.0838689871475,0.0824447967997,0.0829986486016,0.0840272305194,0.0847393256933,0.0856887859252,0.0864008810991,0.0858470292972,0.0857679076112,0.0860052726692,0.0855305425532,0.0865591244711,0.0849766907513,0.0848184473793,0.0832360136596,0.0814953365678,0.0815744582538,0.0822865534277,0.0841854738914,0.0848184473793,0.0835525004035,0.0831568919736,0.0838689871475,0.0826030401717,0.0842645955774,0.0852140558093,0.0852931774953,0.0849766907513,0.0834733787175,0.0852931774953,0.0852140558093,0.0856096642392,0.0852931774953,0.0858470292972,0.0851349341233,0.0847393256933,0.0846602040074,0.0849766907513,0.0844228389494,0.0829195269156,0.0840272305194,0.0837107437755,0.0860052726692,0.0851349341233,0.086717367843,0.0857679076112,0.0853722991812,0.0854514208672,0.0864008810991,0.0875877063889,0.0877459497609,0.0875877063889,0.0856096642392,0.086717367843,0.0841854738914,0.0849766907513,0.0849766907513,0.0848975690653,0.0846602040074,0.0826030401717,0.0819700666838,0.0827612835436,0.0846602040074,0.0851349341233,0.087271219645,0.086717367843,0.086954732901,0.0863217594131,0.086954732901,0.0878250714469,0.0874294630169,0.086717367843,0.0852931774953,0.0860052726692,0.0851349341233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m <- 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ycorr <- 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altd  <- c(3, 46, 62, 174, 274, 351)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('100-FHY3-GSE69422/FHY3-ChIP-seq1-GSM1701005/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) : 3,46,62,174,274,351',bty='n')
dev.off()