# R script for Peak Model
#  -- generated by MACS
p <- c(0.042857820857516604,0.05005183443716782,0.05730668534095985,0.06448341558988924,0.07171821783004395,0.0717043911654665,0.07165807183913202,0.07162143117800175,0.07150666986200885,0.07165046717361441,0.0716228138444595,0.0715156571939842,0.07140020454476242,0.07133037988864627,0.07127645589679418,0.07123497590306181,0.07121423590619562,0.07111330125478019,0.0712681598980477,0.0712453459014949,0.07136425521686103,0.07139259987924483,0.07131378789115332,0.07143477120620607,0.07141264854288214,0.07141057454319552,0.07127023389773432,0.0713089485585512,0.07108426525916751,0.07103172393377317,0.07088377862279438,0.0709266412829845,0.07093217194881549,0.07083261996385778,0.07068951398548111,0.07064734265851985,0.0706743046544459,0.07067015665507266,0.07062452866196706,0.0706183066629072,0.0706819093199635,0.07061623266322058,0.070521520010865,0.07055055600647765,0.07062867666134029,0.07069573598454096,0.0707531166425374,0.0707379073115022,0.07085889062655495,0.07082086729896696,0.07073375931212897,0.0706743046544459,0.07060240599864312,0.07040952402778759,0.07032172470772073,0.07019728472652362,0.07007353607855536,0.07001822942024553,0.06985507477823154,0.06991522076914347,0.06989655477196391,0.06998366275880188,0.07015511339956236,0.07026365271649541,0.07036113070176649,0.07043856002340025,0.07048487934973473,0.07062038066259381,0.07073168531244235,0.07061899799613607,0.07060309733187199,0.070439942689858,0.07038671003123478,0.07022079005630529,0.07007699274469972,0.07001477275410117,0.06990554210393926,0.06972648679766118,0.0696877721368443,0.0696953768023619,0.06960826881552391,0.06972233879828794,0.06976312745879144,0.06988549344030194,0.06985922277760477,0.0697921634544041,0.06972510413120343,0.06974584412806963,0.06973270879672104,0.06969883346850626,0.0697029814678795,0.06973754812932315,0.06963937881082319,0.06947553283558032,0.06957646748699577,0.06964974880925628,0.06974031346223863,0.0697921634544041,0.06983848278073858,0.06978594145534425,0.06989240677259068,0.06981843411710127,0.06975414012681609,0.06970920346693936,0.06954881415784085,0.06941469551143951,0.0693130695267952,0.06926260220108747,0.06916166754967204,0.06919139487851357,0.06913401422051711,0.06904967156659463,0.06906142423148547,0.06925084953619663,0.06936353685250292,0.06937321551770713,0.06947622416880919,0.06943820084122118,0.06950733416410848,0.06955780148981619,0.0695398268258655,0.06957508482053802,0.06964560080988305,0.06954950549106972,0.06955849282304506,0.06972648679766118,0.0698536921117738,0.06972233879828794,0.06960412081615068,0.06944580550673879,0.06945963217131625,0.0694098561788374,0.06940294284654867,0.06932343952522829,0.06928887286378464,0.06917411154779174,0.06902063557098197,0.06911811355625304,0.06919969087726004,0.0692619108678586,0.06923564020516143,0.0692135175418375,0.06925015820296776,0.06927642886566493,0.06931721752616843,0.06932689619137265,0.06940501684623529,0.0694278308427881,0.06957093682116477,0.06960204681646406,0.06963937881082319,0.06963246547853447,0.06948590283401342,0.06959859015031969,0.06951217349671059,0.06941676951112613,0.06941953484404162,0.06938358551614023,0.06937114151802051,0.06924808420328114,0.06928195953149592,0.06930892152742196,0.06934487085532334,0.0693130695267952,0.06938635084905571,0.06931721752616843,0.06918171621330935,0.06926329353431634,0.06914507555217908,0.06917618554747837,0.06911880488948191,0.06917411154779174,0.06926536753400296,0.06932067419231279,0.06926260220108747,0.0694430401738233,0.06950802549733735,0.06939395551457332,0.06939395551457332,0.0694914334998444,0.06939810351394655,0.06930615619450646,0.06918932087882695,0.0690607328982566,0.06907248556314743,0.06906142423148547,0.06892937958477074,0.06904967156659463,0.06900888290609113,0.06902547490358407,0.06907179422991856,0.06909046022709812,0.06919208621174244,0.06927020686660508,0.06926882420014734,0.06924739287005227,0.06938704218228459,0.06934210552240785,0.06932689619137265,0.0693946468478022,0.06940432551300642,0.06943543550830569,0.06938082018322474,0.06940778217915078,0.06954397482523873,0.06962831747916123,0.06968362413747106,0.06958268948605562,0.06955157949075634,0.069580615486369,0.0696366134779077,0.06975759679296045,0.06974031346223863,0.06982119945001676,0.06971888213214357,0.06973893079578089,0.06969745080204852,0.0698025334528372,0.06989240677259068,0.06980184211960833,0.06976520145847806,0.06963868747759432,0.06971127746662598,0.06965251414217177,0.06975967079264708,0.0697410047954675,0.0699553180964181,0.07003413008450961,0.07017654472965743,0.07020074139266798,0.07028231871367498,0.07043302935756926,0.07058235733500581,0.07062936799456916,0.07067499598767478,0.07081049730053386,0.07085405129395285,0.07096189927765702,0.07094254194724858,0.07102066260211122,0.07119211324287168,0.07130341789272023,0.07134628055291034,0.07152671852564617,0.07157580318489613,0.07159377784884684,0.07149284319743139,0.07155022385542784,0.07168365116860032,0.07188690313788894,0.07190418646861076,0.072003047120339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m <- 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ycorr <- 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altd  <- c(186)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('GRCh38.p13-SRX663241_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) : 186',bty='n')
dev.off()