# R script for Peak Model
#  -- generated by MACS
p <- c(0.0479790007999,0.056063078441,0.0642279968585,0.0718674502294,0.0799919482587,0.0799919482587,0.0802748909761,0.0807599356346,0.0808811967992,0.0803557317525,0.0804769929171,0.0799111074823,0.0799111074823,0.0800727890351,0.0799515278705,0.0795069036002,0.0793856424356,0.0786984958361,0.0787389162243,0.0793452220474,0.0791431201064,0.0792239608828,0.0786984958361,0.0786580754479,0.0787389162243,0.0787389162243,0.0786984958361,0.0795473239884,0.0790622793299,0.0786176550597,0.0789410181653,0.0791431201064,0.0790218589417,0.0791835404946,0.0791431201064,0.0792239608828,0.0782538715658,0.0780517696248,0.0786176550597,0.0783751327304,0.0784963938951,0.0786176550597,0.0791431201064,0.0787389162243,0.0786580754479,0.0787793366125,0.0801940501997,0.0800727890351,0.0798706870941,0.0799515278705,0.0801940501997,0.0801940501997,0.0801940501997,0.0808811967992,0.0809216171874,0.0810832987402,0.08063867447,0.08063867447,0.08063867447,0.0809216171874,0.08063867447,0.0809620375756,0.0809620375756,0.0806790948582,0.0802748909761,0.0800323686469,0.0799515278705,0.0793452220474,0.0791026997181,0.0789005977771,0.0788197570007,0.0786176550597,0.0781326104012,0.0780517696248,0.078092190013,0.0781730307894,0.077687986131,0.077890088072,0.0778092472956,0.0780517696248,0.0778092472956,0.0772837822489,0.0777284065192,0.0775667249663,0.0782134511776,0.0782134511776,0.0786984958361,0.0784963938951,0.0789814385535,0.0786984958361,0.0788197570007,0.0793452220474,0.0789005977771,0.0790622793299,0.0784963938951,0.0780517696248,0.077890088072,0.0785368142833,0.077687986131,0.0775263045781,0.0780517696248,0.078294291954,0.0787389162243,0.0793452220474,0.0795877443766,0.0798302667058,0.0795877443766,0.079264381271,0.0799919482587,0.0803557317525,0.0801536298115,0.0800727890351,0.0800727890351,0.079668585153,0.0801132094233,0.0807195152464,0.0809216171874,0.0816491841751,0.0814066618459,0.0818917065043,0.0820533880571,0.08221506961,0.0820533880571,0.0821342288336,0.0820533880571,0.08221506961,0.0826596938802,0.0815279230105,0.0818512861161,0.0810024579638,0.0809216171874,0.0807195152464,0.081042878352,0.081042878352,0.081042878352,0.0807195152464,0.0803557317525,0.0808003560228,0.0808811967992,0.0812854006812,0.0814470822341,0.0811237191284,0.0809216171874,0.0804365725289,0.0798706870941,0.0797090055412,0.0797090055412,0.0797898463176,0.079668585153,0.0794260628238,0.0788197570007,0.0793048016592,0.0792239608828,0.0795877443766,0.0799111074823,0.0798302667058,0.0795069036002,0.079466483212,0.0791835404946,0.0791431201064,0.0793856424356,0.0789005977771,0.079264381271,0.0791026997181,0.0786176550597,0.0786580754479,0.0789410181653,0.079264381271,0.0793856424356,0.0791835404946,0.0788601773889,0.0785368142833,0.0780113492366,0.0780113492366,0.078092190013,0.078294291954,0.0783347123422,0.0776475657428,0.0775667249663,0.0779305084602,0.0780113492366,0.0784963938951,0.0787793366125,0.0783751327304,0.0784559735069,0.0780517696248,0.078092190013,0.0789410181653,0.0789814385535,0.0789410181653,0.0790622793299,0.0790218589417,0.0791026997181,0.0795069036002,0.0796281647648,0.0795473239884,0.0799111074823,0.0795069036002,0.0795877443766,0.0795877443766,0.0799919482587,0.0797898463176,0.0795473239884,0.0798302667058,0.0799515278705,0.0800727890351,0.0799515278705,0.0795069036002,0.0793452220474,0.0793452220474,0.0789005977771,0.0789814385535,0.0790218589417,0.0786984958361,0.0788197570007,0.0789814385535,0.0787389162243,0.0789814385535,0.0793452220474,0.0795069036002,0.079668585153,0.0791431201064,0.0789005977771,0.0790218589417,0.0782538715658,0.0787793366125,0.0789410181653,0.0791431201064,0.0790622793299,0.0791835404946,0.0791026997181,0.0799515278705,0.0803557317525,0.0805578336935,0.0815279230105,0.0810024579638,0.0810832987402,0.081042878352,0.0810832987402,0.0807195152464,0.080840776411,0.0810832987402,0.0810832987402,0.0808811967992,0.0805578336935,0.0804769929171,0.0802344705879,0.0802344705879,0.0798302667058,0.0799111074823,0.0799111074823,0.0794260628238,0.0796281647648,0.0797494259294,0.0801940501997,0.0805982540818,0.0805174133053,0.0811237191284,0.0815279230105,0.0822554899982,0.0821342288336,0.0819725472807,0.0816491841751,0.0816896045633,0.0814470822341,0.0816896045633,0.0820938084454,0.0810024579638,0.0810832987402,0.0809216171874,0.0810832987402,0.0814066618459,0.0815683433987,0.0815279230105,0.0814875026223,0.0814066618459,0.0813258210695,0.0821342288336,0.0816896045633,0.081244980293,0.0814470822341,0.0815279230105,0.0813662414577,0.0815683433987,0.0814470822341,0.081244980293,0.0813662414577,0.0810024579638,0.081042878352,0.0810832987402,0.0812045599048,0.0815279230105,0.0819321268925,0.0820129676689,0.0826596938802,0.082619273492,0.0830234773741,0.0835085220325,0.0839127259146,0.0848828152315,0.0848423948433,0.0845190317377,0.0843169297967,0.0844381909613,0.0839531463028,0.0843977705731,0.0836297831972,0.08379146475,0.0836702035854,0.0832255793151,0.0835489424208,0.0837510443618,0.0836702035854,0.0836297831972,0.083751044361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m <- 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ycorr <- 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altd  <- c(0, 48, 69, 122, 209, 282, 554, 594, 598)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('33-SEP3-AP1-24581456/AP1-ChIP-seq-2d-biological-replicate-2-GSM1279837/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) : 0,48,69,122,209,282,554,594,598',bty='n')
dev.off()