# R script for Peak Model
#  -- generated by MACS
p <- c(0.0193614788094,0.0254756300123,0.0356658820173,0.0407610080197,0.0417800332202,0.0509512600247,0.0529893104256,0.0611415120296,0.0621605372301,0.0601224868291,0.0652176128316,0.0652176128316,0.0611415120296,0.0631795624306,0.0662366380321,0.0601224868291,0.0631795624306,0.0550273608266,0.0519702852252,0.0529893104256,0.0519702852252,0.0570654112276,0.0601224868291,0.0580844364281,0.0591034616286,0.0601224868291,0.0580844364281,0.0601224868291,0.0621605372301,0.0611415120296,0.0580844364281,0.0478941844232,0.0468751592227,0.0478941844232,0.0489132096237,0.0489132096237,0.0417800332202,0.0407610080197,0.0407610080197,0.0438180836212,0.0448371088217,0.0489132096237,0.0438180836212,0.0417800332202,0.0468751592227,0.0478941844232,0.0499322348242,0.0489132096237,0.0489132096237,0.0458561340222,0.0499322348242,0.0468751592227,0.0478941844232,0.0478941844232,0.0458561340222,0.0458561340222,0.0468751592227,0.0499322348242,0.0499322348242,0.0519702852252,0.0509512600247,0.0570654112276,0.0570654112276,0.0601224868291,0.0560463860271,0.0560463860271,0.0570654112276,0.0550273608266,0.0580844364281,0.0591034616286,0.0570654112276,0.0540083356261,0.0580844364281,0.0560463860271,0.0580844364281,0.0550273608266,0.0560463860271,0.0540083356261,0.0570654112276,0.0560463860271,0.0560463860271,0.0570654112276,0.0540083356261,0.0570654112276,0.0550273608266,0.0580844364281,0.0641985876311,0.0672556632326,0.0621605372301,0.0672556632326,0.0652176128316,0.0591034616286,0.0580844364281,0.0529893104256,0.0509512600247,0.0519702852252,0.0468751592227,0.0417800332202,0.0397419828192,0.0366849072178,0.0448371088217,0.0509512600247,0.0529893104256,0.0540083356261,0.0550273608266,0.0550273608266,0.0570654112276,0.0580844364281,0.0591034616286,0.0591034616286,0.0529893104256,0.0550273608266,0.0570654112276,0.0580844364281,0.0631795624306,0.0591034616286,0.0601224868291,0.0601224868291,0.0580844364281,0.0560463860271,0.0560463860271,0.0519702852252,0.0529893104256,0.0580844364281,0.0591034616286,0.0621605372301,0.0580844364281,0.0601224868291,0.0631795624306,0.0621605372301,0.0611415120296,0.0641985876311,0.0570654112276,0.0509512600247,0.0458561340222,0.0438180836212,0.0427990584207,0.0427990584207,0.0397419828192,0.0407610080197,0.0448371088217,0.0458561340222,0.0509512600247,0.0540083356261,0.0529893104256,0.0560463860271,0.0601224868291,0.0621605372301,0.0641985876311,0.068274688433,0.0631795624306,0.0631795624306,0.0601224868291,0.0560463860271,0.0550273608266,0.0560463860271,0.0540083356261,0.0560463860271,0.0560463860271,0.0519702852252,0.0550273608266,0.0489132096237,0.0509512600247,0.0540083356261,0.0540083356261,0.0499322348242,0.0478941844232,0.0438180836212,0.0458561340222,0.0509512600247,0.0468751592227,0.0499322348242,0.0468751592227,0.0509512600247,0.0570654112276,0.0591034616286,0.0611415120296,0.0601224868291,0.0621605372301,0.0611415120296,0.068274688433,0.0662366380321,0.070312738834,0.0662366380321,0.0641985876311,0.0672556632326,0.0641985876311,0.0641985876311,0.0601224868291,0.0591034616286,0.0550273608266,0.0570654112276,0.0601224868291,0.0621605372301,0.0580844364281,0.0591034616286,0.0641985876311,0.0692937136335,0.0692937136335,0.068274688433,0.070312738834,0.076426890037,0.080502990839,0.076426890037,0.0794839656385,0.0754078648365,0.0692937136335,0.0662366380321,0.068274688433,0.0692937136335,0.070312738834,0.0672556632326,0.0611415120296,0.0611415120296,0.0591034616286,0.0560463860271,0.0631795624306,0.0672556632326,0.0692937136335,0.0672556632326,0.0631795624306,0.0621605372301,0.0621605372301,0.0631795624306,0.0652176128316,0.068274688433,0.0662366380321,0.0601224868291,0.0621605372301,0.0652176128316,0.0621605372301,0.0652176128316,0.0631795624306,0.0652176128316,0.0692937136335,0.0692937136335,0.068274688433,0.072350789235,0.068274688433,0.0631795624306,0.068274688433,0.0672556632326,0.0692937136335,0.0631795624306,0.0621605372301,0.0631795624306,0.0631795624306,0.0621605372301,0.0692937136335,0.0754078648365,0.076426890037,0.0774459152375,0.076426890037,0.080502990839,0.076426890037,0.076426890037,0.0754078648365,0.080502990839,0.070312738834,0.0641985876311,0.0601224868291,0.0529893104256,0.0509512600247,0.0519702852252,0.0499322348242,0.0478941844232,0.0529893104256,0.0509512600247,0.0519702852252,0.0570654112276,0.0591034616286,0.0621605372301,0.0672556632326,0.0672556632326,0.072350789235,0.074388839636,0.0672556632326,0.0672556632326,0.0662366380321,0.0631795624306,0.0672556632326,0.0672556632326,0.0662366380321,0.0713317640345,0.0713317640345,0.0662366380321,0.072350789235,0.0713317640345,0.076426890037,0.076426890037,0.076426890037,0.078464940438,0.0825410412399,0.0794839656385,0.0794839656385,0.0845790916409,0.0825410412399,0.0754078648365,0.070312738834,0.0733698144355,0.076426890037,0.0733698144355,0.068274688433,0.068274688433,0.0713317640345,0.0713317640345,0.0713317640345,0.080502990839,0.0906932428439,0.0978264192473,0.0906932428439,0.0927312932449,0.0927312932449,0.0876361672424,0.083560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m <- 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ycorr <- 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altd  <- c(93)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('48-PIF1-PIF4-GSE43286/PIF4-peaks-2-GSM1059964/all.1x36mers.TAIR10.unique.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) : 93',bty='n')
dev.off()