# R script for Peak Model
#  -- generated by MACS
p <- c(0.033255041241771345,0.038959251032236145,0.04452963771911233,0.050451310052908635,0.05590460152414478,0.05587114574824763,0.05553658798927608,0.05568713898081328,0.055369309109790314,0.05575405053260759,0.0556034995410704,0.0554529485495332,0.056038424627733396,0.05553658798927608,0.05563695531696755,0.05540276488568747,0.05548640432543035,0.055837689972350474,0.055887873636196204,0.05550313221337893,0.05602169673978482,0.05590460152414478,0.05568713898081328,0.05585441786029905,0.055887873636196204,0.05694173057695656,0.05690827480105941,0.05669081225772791,0.05695845846490514,0.056874819025162254,0.056356254498756364,0.05694173057695656,0.05659044493003645,0.05643989393849925,0.056088608291579134,0.05521875811825312,0.055252213894150276,0.05557004376517324,0.05516857445440739,0.0550849350146645,0.055519860101327506,0.05503475135081877,0.05506820712671592,0.055419492773636045,0.05630607083491063,0.057075553680545184,0.057594118206951074,0.05709228156849376,0.05777812497438542,0.057995587517716926,0.05737665566361957,0.05737665566361957,0.0575773903190025,0.057995587517716926,0.057276288335928106,0.0575773903190025,0.05702537001669945,0.057125737344390914,0.05709228156849376,0.05719264889618522,0.057594118206951074,0.05735992777567099,0.05754393454310534,0.05710900945644234,0.05784503652617973,0.05690827480105941,0.05680790747336795,0.056925002689007985,0.056607172817985024,0.05622243139516775,0.05595478518799051,0.05617224773132202,0.055938057300041935,0.05578750630850474,0.05513511867851023,0.05521875811825312,0.05555331587722466,0.05585441786029905,0.05580423419645332,0.056188975619270595,0.056506805490293556,0.0569919142408023,0.05702537001669945,0.0572093767841338,0.05771121342259111,0.058112682733356964,0.058831981915145784,0.05802904329361408,0.0580123154056655,0.058514152044122816,0.058229777948997,0.0583803289405342,0.05848069626822566,0.0585977914838657,0.05889889346694009,0.05853087993207139,0.057945403853871195,0.05834687316463705,0.05843051260437993,0.058263233724894156,0.059149811786168745,0.05864797514771143,0.05831341738873989,0.05777812497438542,0.05714246523233949,0.05690827480105941,0.05715919312028807,0.05695845846490514,0.05685809113721368,0.05637298238670494,0.05620570350721917,0.05643989393849925,0.05702537001669945,0.05702537001669945,0.057393383551568145,0.05714246523233949,0.056757723809522216,0.05762757398284823,0.057995587517716926,0.058781798251300046,0.0583803289405342,0.058363601052585624,0.05784503652617973,0.05839705682848278,0.05787849230207688,0.05849742415617424,0.05876507036335147,0.05791194807797404,0.057995587517716926,0.0572093767841338,0.05702537001669945,0.05677445169747079,0.05654026126619072,0.056088608291579134,0.056088608291579134,0.05638971027465352,0.05597151307593909,0.056657356481830755,0.05680790747336795,0.056707540145676485,0.05695845846490514,0.05697518635285372,0.05761084609489965,0.05735992777567099,0.057594118206951074,0.05771121342259111,0.057995587517716926,0.05827996161284273,0.057426839327465305,0.05776139708643684,0.05784503652617973,0.05797885962976835,0.05792867596592262,0.05903271657052871,0.05876507036335147,0.057895220190025465,0.05797885962976835,0.05746029510336246,0.05804577118156266,0.05834687316463705,0.058330145276688464,0.05853087993207139,0.05831341738873989,0.05771121342259111,0.05784503652617973,0.058581063595917124,0.05831341738873989,0.05817959428515127,0.058229777948997,0.05849742415617424,0.05792867596592262,0.058229777948997,0.057995587517716926,0.057895220190025465,0.05829668950079131,0.058162866397202695,0.05903271657052871,0.059568008984883174,0.05884870980309436,0.05869815881155716,0.05903271657052871,0.05869815881155716,0.05926690700180879,0.05978547152821468,0.05965164842462606,0.059668376312574635,0.05953455320898602,0.058932349242837245,0.059300362777705944,0.05889889346694009,0.0593338185536031,0.059400730105397405,0.059450913769243136,0.059752015752317526,0.06003638984744333,0.0609396957966665,0.060488042822054916,0.060688777477437846,0.06124079777974089,0.06155862765076386,0.06149171609896954,0.061525171874866696,0.060688777477437846,0.06027058027872342,0.06006984562334049,0.0593338185536031,0.059568008984883174,0.0599862061835976,0.059869110967957564,0.06027058027872342,0.06047131493410634,0.06020366872692911,0.061474988211020966,0.06159208342666101,0.062194287392809786,0.061792818082043934,0.06169245075435247,0.06182627385794109,0.0617426344181982,0.060906240020769345,0.06078914480512931,0.06083932846897504,0.059919294631803295,0.060086573511289064,0.059400730105397405,0.059969478295649026,0.06032076394256915,0.059618192648728904,0.05938400221744883,0.05960146476078033,0.06012002928718622,0.060220396614877686,0.060554954373849224,0.05993602251975187,0.06003638984744333,0.05985238308000899,0.059099628122323014,0.05960146476078033,0.06005311773539191,0.06070550536538642,0.06065532170154069,0.06062186592564353,0.060437859158209185,0.061006607348460806,0.061675722866403895,0.061843001745889664,0.06267939614331852,0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m <- 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ycorr <- 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altd  <- c(89)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('H526_SOX9_S15_R1_001.fastq.gz_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) : 89',bty='n')
dev.off()