# R script for Peak Model
#  -- generated by MACS
p <- c(0.0230888443673,0.0277589886912,0.0306723731175,0.034567797238,0.0387032755061,0.0400672195259,0.0391288260403,0.0389869758622,0.0391615606968,0.0389651527579,0.0394670841572,0.0399253693479,0.0409183205943,0.0415075444108,0.0409619668029,0.0408092050727,0.0419658296015,0.0420203873623,0.0422277068533,0.0429478692958,0.0419549180493,0.0408092050727,0.0419003602885,0.0418567140799,0.0415293675152,0.0419549180493,0.0420640335709,0.0427296382526,0.0431879234432,0.0424786725529,0.0422822646141,0.0426750804918,0.0415402790673,0.0403836545385,0.041725775454,0.0408092050727,0.0409292321464,0.0403072736734,0.0390306220709,0.0398380769306,0.0401545119432,0.0393579686356,0.0390851798317,0.039521641918,0.0389978874144,0.0390197105187,0.0384850444629,0.0398380769306,0.0411911093982,0.040831028177,0.0407000895511,0.0422822646141,0.0433952429343,0.0440608476159,0.0441263169289,0.0436025624253,0.0441044938246,0.0429151346393,0.0425986996267,0.0428496653263,0.0431442772346,0.0416275714846,0.0408419397292,0.0409074090421,0.0412129325026,0.0429478692958,0.0431333656824,0.0437989703641,0.0441808746897,0.0435261815602,0.0432752158605,0.0432097465476,0.0429478692958,0.0423913801357,0.0425223187616,0.0413875173371,0.0409292321464,0.0413329595763,0.0414748097544,0.0421622375403,0.0414857213065,0.0431115425781,0.0439189974379,0.0442681671069,0.0442681671069,0.0441044938246,0.044344547972,0.0436789432904,0.0422713530619,0.0423259108227,0.0429369577436,0.0413984288893,0.0407110011033,0.0402199812561,0.0401763350475,0.0402745390169,0.0409947014594,0.0407437357597,0.0418021563191,0.0423149992706,0.0426314342832,0.0433188620691,0.0437335010512,0.0450428873102,0.0443881941807,0.0449119486843,0.0449337717886,0.0460358385566,0.0454357031879,0.0450756219667,0.0448355678192,0.0451956490404,0.0459158114829,0.0466359739253,0.0471924630854,0.0472251977419,0.0472142861897,0.0471051706681,0.048130856571,0.0483490876142,0.0481635912275,0.0486546110746,0.047989006393,0.0467014432383,0.0473124901591,0.0478253331106,0.0476834829325,0.0479126255279,0.0472906670548,0.0467232663426,0.0482945298534,0.0483163529577,0.0485564071052,0.0490692500567,0.0490692500567,0.0483818222707,0.0482181489883,0.0481526796753,0.0486218764182,0.0495384467995,0.04888375367,0.0480762988102,0.048130856571,0.0478908024235,0.0487309919397,0.0485127608966,0.04888375367,0.0486000533138,0.0487855497005,0.0486000533138,0.0497348547383,0.0500294666466,0.0507823637455,0.0504113709722,0.0491238078175,0.0501385821682,0.0505423095981,0.0513279413535,0.0513061182491,0.0510005947887,0.049713031634,0.0499749088858,0.0498112356034,0.0505532211502,0.0509133023714,0.0518080496484,0.0521135731089,0.051229737384,0.0511970027276,0.0520481037959,0.052124484661,0.0529428510729,0.0525500351952,0.0529974088337,0.0542958835406,0.0539030676629,0.0536739250675,0.0536848366197,0.0538703330064,0.0535757210981,0.0538266867978,0.053084701251,0.0536739250675,0.052670062269,0.051437056875,0.0513606760099,0.0508369215063,0.0512406489362,0.0518844305135,0.0520371922438,0.0527027969254,0.0533684016071,0.0528664702078,0.0538812445585,0.054186768019,0.0538812445585,0.0535975442024,0.0537939521413,0.0531283474596,0.053084701251,0.0528555586556,0.0523536272564,0.0536739250675,0.0533793131593,0.0536193673067,0.0538266867978,0.0559871741251,0.0562599629291,0.0571110639975,0.057078329341,0.0563036091377,0.0565545748374,0.0564672824201,0.057700287814,0.0573838528014,0.0571547102061,0.0557798546341,0.0554852427258,0.055288834787,0.0556052697996,0.0569910369237,0.0575475260838,0.0568928329543,0.0571110639975,0.0577875802313,0.0588132661342,0.0591187895946,0.059489782368,0.0599153329022,0.0607009646576,0.05990442135,0.0587587083734,0.0584750080173,0.0580712805874,0.0573402065928,0.0558998817079,0.0555070658302,0.0551906308176,0.0551688077132,0.0543395297492,0.0543067950927,0.0547432571791,0.0555943582474,0.0548196380442,0.0550596921917,0.0560744665424,0.055561623591,0.055016045983,0.054328618197,0.0547214340747,0.0551142499525,0.0555179773823,0.0543722644057,0.055430684965,0.0551906308176,0.0551251615046,0.0566746019111,0.057220179519,0.0568382751935,0.0565763979417,0.0566746019111,0.0566091325982,0.056805540537,0.0555725351431,0.0563472553464,0.0567400712241,0.0559871741251,0.0556925622169,0.055288834787,0.0547650802834,0.0546450532096,0.0547214340747,0.0549069304614,0.0550487806395,0.0546232301053,0.0545577607924,0.0549942228787,0.0550924268481,0.0569255676108,0.0579512535137,0.0576566416054,0.0571001524453,0.0578203148878,0.0576239069489,0.0581367499004,0.0581040152439,0.0578966957529,0.0584313618086,0.0565545748374,0.0556052697996,0.055496154278,0.0558016777384,0.05591079326,0.0566964250154,0.0556052697996,0.0547650802834,0.0544377337186,0.0547214340747,0.0566855134633,0.0576566416054,0.0596643672025,0.0634070295929,0.0674443038915,0.0713069933556,0.0762935726921,0.0822949263792,0.0883944840358,0.0939375525323,0.0984876697824,0.105831144385,0.10823168586,0.108919113646,0.10853720932,0.109060963824,0.109955711101,0.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m <- 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ycorr <- 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altd  <- c(78, 173, 318, 525)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Oct4-DamID-r2-GSM1562328.36mers.unique.pseudoRep2.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) : 78,173,318,525',bty='n')
dev.off()