# R script for Peak Model
#  -- generated by MACS
p <- c(0.0115287231975,0.0139214770687,0.0160242001676,0.0182719386527,0.0202296463655,0.0194320617418,0.0184169540388,0.0191420309695,0.0192145386626,0.0201571386724,0.0193595540487,0.0189970155834,0.0188520001972,0.0188520001972,0.0189245078903,0.0183444463458,0.0187069848111,0.0187794925042,0.0192870463556,0.0190695232764,0.0201571386724,0.0197946002071,0.0189245078903,0.0179819078804,0.017474354029,0.0180544155735,0.0180544155735,0.0177643848012,0.0179094001874,0.0181994309596,0.0173293386428,0.0181994309596,0.0193595540487,0.0200121232863,0.0205196771377,0.0215347848407,0.0214622771476,0.0219698309991,0.0224773848505,0.0219698309991,0.0223323694644,0.0223323694644,0.0226224002367,0.0224048771575,0.0221873540783,0.0216072925337,0.0216072925337,0.0208822156031,0.0207372002169,0.0211722463753,0.0203746617516,0.0200846309793,0.0193595540487,0.0197946002071,0.0205196771377,0.0206646925239,0.0210272309892,0.02080970791,0.0201571386724,0.0200121232863,0.0210997386823,0.0217523079199,0.0217523079199,0.0210997386823,0.0213897694545,0.0213172617615,0.0212447540684,0.0220423386921,0.0221873540783,0.0221148463852,0.0215347848407,0.0205196771377,0.0212447540684,0.0214622771476,0.0207372002169,0.0196495848209,0.0192870463556,0.0197946002071,0.0193595540487,0.0199396155932,0.0201571386724,0.0202296463655,0.019722092514,0.0203746617516,0.0203021540585,0.0207372002169,0.0213897694545,0.0203746617516,0.0210997386823,0.0197946002071,0.0196495848209,0.0189245078903,0.018561969425,0.0181994309596,0.0179819078804,0.0181994309596,0.0180544155735,0.0182719386527,0.0174018463359,0.0178368924943,0.0189245078903,0.0198671079001,0.019722092514,0.0190695232764,0.0192870463556,0.0194320617418,0.0187069848111,0.0179094001874,0.0183444463458,0.0190695232764,0.0181269232666,0.0176193694151,0.0182719386527,0.0187069848111,0.0184894617319,0.018634477118,0.0190695232764,0.0195770771279,0.0196495848209,0.0192145386626,0.0192145386626,0.0193595540487,0.0189245078903,0.0197946002071,0.0195770771279,0.0192870463556,0.0189970155834,0.0196495848209,0.0191420309695,0.0200121232863,0.0197946002071,0.0208822156031,0.02080970791,0.0207372002169,0.0213172617615,0.0213897694545,0.0210997386823,0.0207372002169,0.0210997386823,0.0199396155932,0.0203746617516,0.0194320617418,0.0193595540487,0.0187069848111,0.018561969425,0.0187794925042,0.0193595540487,0.0192870463556,0.0195770771279,0.0203021540585,0.0205921848308,0.0210997386823,0.0215347848407,0.0213172617615,0.0213897694545,0.0207372002169,0.0210997386823,0.0218248156129,0.0213172617615,0.0213172617615,0.0213897694545,0.0205921848308,0.0205921848308,0.02080970791,0.0205196771377,0.0207372002169,0.0195770771279,0.0196495848209,0.019722092514,0.0199396155932,0.0189245078903,0.0192870463556,0.0196495848209,0.0196495848209,0.0196495848209,0.019722092514,0.0200846309793,0.0198671079001,0.0200846309793,0.019722092514,0.0202296463655,0.0203746617516,0.0198671079001,0.0203746617516,0.0214622771476,0.0219698309991,0.0230574463951,0.0226224002367,0.0223323694644,0.0224048771575,0.0229124310089,0.0224048771575,0.0230574463951,0.0229124310089,0.0215347848407,0.0215347848407,0.0200846309793,0.0200846309793,0.0203746617516,0.0201571386724,0.0195770771279,0.0197946002071,0.0184894617319,0.0179819078804,0.0182719386527,0.0180544155735,0.0182719386527,0.0176918771082,0.0172568309498,0.0168217847914,0.0166042617122,0.0169668001775,0.0178368924943,0.0181269232666,0.018634477118,0.018561969425,0.0189970155834,0.0192145386626,0.0196495848209,0.019722092514,0.0198671079001,0.0195770771279,0.0200121232863,0.0195045694348,0.0192145386626,0.0188520001972,0.0187794925042,0.0190695232764,0.0194320617418,0.0198671079001,0.0202296463655,0.019722092514,0.0189245078903,0.0200121232863,0.0202296463655,0.0203021540585,0.0203746617516,0.0209547232961,0.0200121232863,0.0200121232863,0.0200846309793,0.0203021540585,0.0208822156031,0.0210272309892,0.0209547232961,0.0207372002169,0.0205196771377,0.0200846309793,0.0201571386724,0.0197946002071,0.0194320617418,0.0203021540585,0.019722092514,0.0189245078903,0.0187794925042,0.0191420309695,0.0189970155834,0.0192145386626,0.0195045694348,0.0192870463556,0.0195045694348,0.0192870463556,0.0192145386626,0.0190695232764,0.0189245078903,0.0196495848209,0.019722092514,0.0191420309695,0.0194320617418,0.019722092514,0.0197946002071,0.0192870463556,0.0196495848209,0.0200846309793,0.0196495848209,0.0190695232764,0.0193595540487,0.0187069848111,0.0179819078804,0.0177643848012,0.0176193694151,0.017546861722,0.0168942924844,0.0166042617122,0.0177643848012,0.0174018463359,0.0170393078706,0.0184169540388,0.0187794925042,0.0192145386626,0.019722092514,0.0204471694447,0.0214622771476,0.0207372002169,0.0196495848209,0.019722092514,0.0203021540585,0.0199396155932,0.0200121232863,0.02080970791,0.0321934157214,0.0527856005522,0.0730152469177,0.0953476163821,0.118042524312,0.141897555331,0.165752586349,0.191202786616,0.21708803304,0.240217987128,0.253341879573,0.257837356544,0.261245218118,0.26414552584,0.26465307969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m <- 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ycorr <- 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altd  <- c(12, 294)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('JA26-1417-Foxg1-ChIP.2x36mers.hg19-male.unique.dedup.MACS2_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) : 12,294',bty='n')
dev.off()