# R script for Peak Model
#  -- generated by MACS
p <- c(0.0384520468541,0.0448875643413,0.0512867870524,0.0577086939985,0.0643120748251,0.0639990323813,0.0640625482394,0.0642122641909,0.0642417536964,0.0640670850865,0.064280316896,0.0642735116255,0.0641986536498,0.0642009220733,0.0639241744056,0.0643982749184,0.0644890118586,0.0646069698809,0.0643892012243,0.0645865540694,0.0647067805152,0.0646863647037,0.0649086702073,0.0651400494049,0.0653011074738,0.0649086702073,0.0650674598527,0.064808859573,0.0650198229591,0.0646727541626,0.0645865540694,0.0646523383511,0.0645593329873,0.064253095814,0.0642916590136,0.0643733222598,0.0643166116721,0.0643960064949,0.0643597117188,0.0646364593865,0.064445911812,0.0644096170359,0.0645616014108,0.0646069698809,0.0645525277168,0.0646886331272,0.0646931699742,0.0649064017838,0.0647861753379,0.0650357019236,0.065180881028,0.0652012968396,0.065185417875,0.0650266282296,0.0651309757109,0.0652262494981,0.0651445862519,0.0651740757575,0.0652353231922,0.0651241704404,0.0650266282296,0.0651014862053,0.0648950596662,0.0650039439945,0.0649517702539,0.064822470114,0.0649336228658,0.0648837175487,0.0649426965599,0.0645797487989,0.0645956277634,0.0645978961869,0.0647521489853,0.0649495018304,0.0649721860654,0.0648678385842,0.064799785879,0.0646455330805,0.0648814491252,0.0653101811679,0.0654009181081,0.0652081021101,0.0651559283694,0.0651060230523,0.0651082914758,0.0651355125579,0.06481339642,0.0647498805618,0.0643982749184,0.0643120748251,0.0642190694614,0.0642553642375,0.0641668957207,0.0644141538829,0.0643937380714,0.0643710538363,0.0646909015507,0.0648927912427,0.0651037546288,0.0650039439945,0.0651355125579,0.0652353231922,0.0656232236117,0.0652239810746,0.0654258707667,0.0654281391902,0.0652443968862,0.0651990284161,0.0650288966531,0.0650674598527,0.0652693495448,0.065171807334,0.0648111279965,0.0651377809814,0.065010749265,0.0652239810746,0.0654236023432,0.0656912763169,0.0657978922217,0.0658750186209,0.0657638658691,0.0661109346656,0.0663808770628,0.0664761508501,0.0663967560274,0.0664602718855,0.0666077194134,0.0663763402158,0.066641745766,0.0666893826597,0.0667619722119,0.0666984563537,0.066632672072,0.0664965666616,0.0667801195999,0.0667392879768,0.0668050722585,0.0670614041147,0.0669434460924,0.0668277564935,0.0667007247772,0.0667120668947,0.0667279458593,0.0665532772493,0.0663604612513,0.0661812557943,0.0661631084062,0.0660111240313,0.0659975134903,0.0660837135835,0.0661699136767,0.0664126349919,0.0665963772959,0.0667528985178,0.0670931620438,0.0673744465585,0.0675967520622,0.0676920258494,0.0678462786478,0.0679891893287,0.0680776578455,0.0680390946459,0.06809353681,0.0684678266885,0.0683407949722,0.0685721741698,0.0685699057463,0.0685086583117,0.0688217007555,0.0689010955782,0.068980490401,0.0687014743097,0.0686992058862,0.0684995846176,0.0686062005224,0.0689396587778,0.0688511902611,0.0691596958579,0.0691324747759,0.0690576168002,0.0692572380687,0.0696995806524,0.0696428700648,0.0699513756616,0.0699649862027,0.0694591277608,0.0695135699249,0.0696201858297,0.0693547802795,0.0698220755218,0.0698198070983,0.0698878598034,0.0699400335441,0.0699785967437,0.0704390867155,0.0708383292526,0.0710311452506,0.0711286874614,0.0715687616216,0.0715755668921,0.0717910671252,0.0718477777128,0.072274241332,0.0720405937109,0.0720020305112,0.0721018411455,0.0722220675914,0.0723241466491,0.0721812359682,0.0722129938973,0.0723196098021,0.0723672466958,0.0722492886734,0.0726734838691,0.0727324628803,0.0726621417516,0.0727279260332,0.0726916312571,0.0728322735145,0.0728141261265,0.0728731051376,0.0728776419847,0.0730069421245,0.0730160158185,0.0729298157253,0.0730795316767,0.0732383213221,0.0734402110142,0.0734787742138,0.0735490953425,0.0735218742604,0.0738122324692,0.0743090172171,0.0743929488868,0.0745472016852,0.0748942704817,0.074998617963,0.0751233812558,0.0754069341941,0.0757721503786,0.0761328297161,0.0762144929623,0.0758628873189,0.0762485193149,0.0764912406301,0.0764095773839,0.076091998093,0.0764980459006,0.0764753616655,0.0762054192683,0.0760126032703,0.0761305612926,0.0764254563484,0.0764141142309,0.0764844353596,0.0766545671225,0.0772647730457,0.0770901044357,0.0775914260306,0.0779271527095,0.0785056007036,0.0789887749104,0.0791316855913,0.0796511545743,0.0797940652551,0.0801297919341,0.080107107699,0.0801796972512,0.0800390549938,0.0800685444994,0.0799641970181,0.0797986021022,0.080088960311,0.0799732707121,0.0802114551803,0.0802364078389,0.0803067289676,0.0807740242098,0.0812889563458,0.0816156093307,0.0820806361494,0.0822008625953,0.0821691046662,0.0823346995821,0.0825161734626,0.08283148433,0.0834303481356,0.0833532217364,0.0835074745348,0.0835732588165,0.0835505745815,0.0836776062978,0.0841449015401,0.0842605911389,0.0841993437042,0.0841471699636,0.0844103070903,0.0849932919314,0.0852246711291,0.0861955563897,0.0868851571356,0.0877403527975,0.0882734323214,0.0891535806419,0.0905032926281,0.0919301310135,0.0928874057331,0.0938061172531,0.0948745447246,0.0955437296589,0.0964306832498,0.0969909838559,0.0975853108145,0.098141074573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m <- 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ycorr <- 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altd  <- c(244)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Sarcophilus_harrisii-male-liver-H3K27Ac-ERR572156.50mers.unique.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) : 244',bty='n')
dev.off()