# R script for Peak Model
#  -- generated by MACS
p <- c(0.0563601540427,0.0649767819121,0.0739882198446,0.0835450654929,0.0930408580387,0.0929391028678,0.0916691983353,0.0904155746302,0.091258107445,0.0901672920132,0.0902161344953,0.09170175999,0.0920436573641,0.0914371965457,0.0920843594325,0.0936717400981,0.0945671856018,0.0952306293158,0.0945061324992,0.094856170287,0.0948602404939,0.0950026977331,0.094388096501,0.0942700605028,0.0933624043786,0.092120991294,0.0913395115817,0.0912662478587,0.0920029552958,0.0915145304756,0.0908022442795,0.088176960871,0.0874483938475,0.0867727395129,0.0868337926155,0.0867401778583,0.0866465631011,0.0860970851784,0.0857755388384,0.086129646833,0.0855801689103,0.0873059366083,0.0892311444412,0.0891823019592,0.0890683361678,0.0889136683081,0.0887834216894,0.0885025774178,0.0880670652864,0.0868622840633,0.0862151211766,0.0852016396747,0.0836834525253,0.0840945434156,0.0833619061853,0.0826699710234,0.0822344588921,0.0822059674442,0.0825844966799,0.0831095533616,0.0840294201062,0.0833741168058,0.0832805020486,0.0843753876872,0.0839724372105,0.0850632526423,0.0846073894768,0.0850836036765,0.0849411464373,0.0853807287754,0.0844201599624,0.0849167251962,0.0846562319588,0.0830688512932,0.0835125038382,0.0831217639821,0.0832316595666,0.0821896866169,0.0814774004208,0.0806674292606,0.0814407685592,0.0812535390448,0.0825356541978,0.0825519350252,0.0822059674442,0.0827432347464,0.08250716275,0.0834555209425,0.0846643723725,0.0847213552682,0.0844812130649,0.0848027594049,0.0835572761134,0.0840986136224,0.084306194171,0.0842166496206,0.085539466842,0.0844527216171,0.0831502554299,0.0840619817609,0.0840660519677,0.0841922283796,0.0839968584516,0.0831624660504,0.0831787468777,0.0821489845485,0.0814733302139,0.0826455497824,0.0828042878489,0.0827188135054,0.0826211285414,0.082136773928,0.0825967073004,0.0824868117158,0.0824949521295,0.0821652653759,0.0818437190359,0.0819332635863,0.0819129125521,0.0812901709064,0.0812291178038,0.0817948765539,0.0819414039999,0.0826781114371,0.0824623904748,0.0822059674442,0.0823199332356,0.0816646299352,0.0814204175251,0.0819576848273,0.0823931969586,0.082877551572,0.0823606353039,0.0825030925432,0.0828368495036,0.0835369250792,0.0843346856189,0.0846073894768,0.0846684425793,0.0851975694678,0.0850998845038,0.0839276649354,0.0845666874084,0.08428177293,0.0839032436944,0.0845015640991,0.0843835281009,0.083862541626,0.0838096289372,0.0834351699083,0.0848068296117,0.0860482426963,0.0859220662845,0.0858569429751,0.0860726639373,0.0866791247557,0.0859627683528,0.0867849501335,0.0883926818332,0.0888933172739,0.0881199779753,0.0869274073727,0.0864552633798,0.086821581995,0.0870861454392,0.08637792945,0.0872286026785,0.0870902156461,0.0854865541531,0.0849167251962,0.0832153787393,0.0840823327951,0.083467731563,0.0841474561044,0.0838259097645,0.0831583958436,0.0827310241259,0.0827717261943,0.0836468206638,0.083492152804,0.0843631770667,0.0833619061853,0.0837282248005,0.0824705308885,0.082409477786,0.0827961474353,0.0829833769497,0.0830525704659,0.0822751609604,0.0820920016528,0.0822995822014,0.0832153787393,0.0834107486673,0.083862541626,0.08428177293,0.0830810619137,0.0814611195934,0.080016196167,0.0792021548001,0.078241585987,0.0769146985589,0.0764466247728,0.0769961026956,0.0763530100156,0.0753476689274,0.0752581243771,0.075160439413,0.0751319479652,0.0759052872638,0.0759297085048,0.0760151828483,0.0751482287925,0.073731796814,0.0730602126862,0.0733695484057,0.0734957248175,0.0740370623266,0.0742894151504,0.0742894151504,0.0740045006719,0.0745132765263,0.0744522234237,0.0749121567961,0.0749854205191,0.0743016257709,0.0745458381809,0.0741876599795,0.0733247761305,0.0723153648354,0.0725270155908,0.0715094638821,0.0711024431986,0.0701785062471,0.0699465044575,0.0693156223981,0.0683550535851,0.0683957556534,0.0685911255815,0.0690999014359,0.0683143515167,0.0688475486121,0.0694580796373,0.0706587906536,0.0705936673443,0.0707198437562,0.0711105836123,0.0709233540979,0.0712856025062,0.0710495305098,0.0726043495207,0.0725188751772,0.0720141695297,0.0707320543767,0.0708948626501,0.0721159247005,0.0725880686934,0.0725148049703,0.0726491217959,0.0725636474524,0.0716030786393,0.0716682019487,0.0717536762922,0.0717699571196,0.0718432208426,0.0707808968587,0.0707035629288,0.0708093883065,0.0703820165889,0.0709803369936,0.0708663712022,0.0714524809864,0.0719775376681,0.0725025943498,0.0720100993228,0.071289672713,0.0707157735493,0.0706872821015,0.0712937429199,0.0704593505187,0.0701540850061,0.0693603946733,0.0692871309503,0.0694987817057,0.0699465044575,0.0713873576771,0.0719693972545,0.0718717122904,0.0715908680188,0.0716397105008,0.0722705925602,0.0729381064812,0.0731253359956,0.0736951649525,0.0745010659058,0.0743504682529,0.0738742540532,0.0737969201233,0.0742120812205,0.075062754449,0.0756081621649,0.0759907616073,0.0762186931901,0.0762878867063,0.0759459893322,0.0766338542872,0.0779810927496,0.0784695175698,0.0786770981184,0.0789701530105,0.0787422214277,0.0789660828036,0.0789172403216,0.0793690332803,0.0802278469225,0.0802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m <- 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ycorr <- 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xcorr <- 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altd  <- c(173, 350, 540, 590)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('S7KO-H3K4me3_snap-chip_control-vs-S7KO-IgG.2x25mers.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) : 173,350,540,590',bty='n')
dev.off()