# R script for Peak Model
#  -- generated by MACS
p <- c(0.0486262186545,0.0566329454209,0.0646117741846,0.0728416849724,0.0812947797815,0.0815458618056,0.0817969438296,0.0821317198616,0.0822154138697,0.082187515867,0.0820480258536,0.0822433118723,0.082438597891,0.0827175779177,0.0824943938964,0.0823270058803,0.0817690458269,0.0815737598082,0.0812947797815,0.0811552897682,0.0810157997548,0.0807089217255,0.0800393696614,0.0790629395679,0.0784212855065,0.0781423054798,0.0785328775172,0.0780865094744,0.0782538974905,0.0778075294477,0.0777517334424,0.0778912234557,0.0783375914985,0.0787002655332,0.0790350415652,0.0789513475572,0.0784212855065,0.0784491835092,0.0782817954931,0.0785886735225,0.0785607755198,0.0783375914985,0.0781702034825,0.0783654895011,0.0783096934958,0.0784491835092,0.0783096934958,0.0786444695278,0.0787839595412,0.0787839595412,0.0790350415652,0.0787839595412,0.0790071435626,0.0787560615385,0.0792582255866,0.0791187355732,0.0794535116053,0.0792582255866,0.0792861235893,0.0793140215919,0.0790350415652,0.0795093076106,0.0793698175973,0.0799277776507,0.0799277776507,0.0800951656667,0.0802625536827,0.0806252277174,0.0807089217255,0.0805973297148,0.0807647177308,0.0808205137361,0.0808484117388,0.0805694317121,0.080067267664,0.0800393696614,0.0798719816453,0.079732491632,0.0799556756534,0.0801509616721,0.0801788596747,0.0800393696614,0.0804299416988,0.0803462476907,0.0806252277174,0.0805415337094,0.0806252277174,0.0805694317121,0.0800114716587,0.079732491632,0.0797603896347,0.0797045936293,0.0795930016186,0.079565103616,0.0793977155999,0.0796766956267,0.0797045936293,0.0798719816453,0.0802904516854,0.0805415337094,0.0804020436961,0.0803462476907,0.0802904516854,0.0802067576774,0.0801509616721,0.0800393696614,0.0795930016186,0.0793419195946,0.0788955515519,0.0786723675305,0.0790908375706,0.0792861235893,0.0788397555465,0.0786165715252,0.0786444695278,0.0786444695278,0.0790908375706,0.0791466335759,0.0793698175973,0.0792024295813,0.0788397555465,0.0785886735225,0.0791466335759,0.0792861235893,0.0791745315786,0.0790629395679,0.0785328775172,0.0780586114718,0.0780586114718,0.0783096934958,0.0782817954931,0.0782259994878,0.0780028154664,0.0780028154664,0.0778633254531,0.0776680394344,0.0779749174638,0.0785049795145,0.0785886735225,0.0784491835092,0.0783654895011,0.0785886735225,0.0785886735225,0.0790908375706,0.0789792455599,0.0791745315786,0.0791187355732,0.0790629395679,0.0791187355732,0.0793698175973,0.0795930016186,0.0793977155999,0.0793419195946,0.0792303275839,0.0798440836427,0.0799556756534,0.079732491632,0.07981618564,0.079899879648,0.0796766956267,0.07981618564,0.0801788596747,0.079983573656,0.0797882876373,0.0794256136026,0.0792582255866,0.079648797624,0.0796208996213,0.0794256136026,0.0795093076106,0.0792024295813,0.0792303275839,0.0790071435626,0.0786165715252,0.0790350415652,0.0790350415652,0.0789513475572,0.0787002655332,0.0786723675305,0.0786723675305,0.0786444695278,0.0784212855065,0.0790908375706,0.0793698175973,0.0788955515519,0.0789234495546,0.0792861235893,0.0793698175973,0.0797045936293,0.079565103616,0.079732491632,0.0796208996213,0.0794535116053,0.0790629395679,0.0795093076106,0.0797045936293,0.0794535116053,0.0792861235893,0.0793140215919,0.079648797624,0.0794256136026,0.0792024295813,0.0793977155999,0.079899879648,0.0800393696614,0.0802067576774,0.0799556756534,0.0800393696614,0.079648797624,0.079565103616,0.079732491632,0.0799556756534,0.0799556756534,0.0800114716587,0.07981618564,0.0801230636694,0.0803741456934,0.0807089217255,0.0811273917655,0.0803462476907,0.0802067576774,0.0802346556801,0.0798440836427,0.0800393696614,0.0797603896347,0.0792303275839,0.0790350415652,0.0789234495546,0.0784491835092,0.0791466335759,0.0795930016186,0.0797603896347,0.0800951656667,0.0797603896347,0.0801230636694,0.0804020436961,0.0807089217255,0.0800393696614,0.0802904516854,0.0799277776507,0.0796766956267,0.0798440836427,0.0797045936293,0.0802346556801,0.0800393696614,0.0798440836427,0.0801230636694,0.0806252277174,0.0806810237228,0.0812947797815,0.0809879017522,0.0810994937628,0.0812947797815,0.0808205137361,0.0810436977575,0.0809879017522,0.0805973297148,0.0809321057468,0.0807926157335,0.0806531257201,0.0808763097415,0.0806810237228,0.0802346556801,0.0802625536827,0.0799277776507,0.0799556756534,0.0800114716587,0.0800951656667,0.0801788596747,0.0800951656667,0.0801230636694,0.0804020436961,0.0807926157335,0.0807647177308,0.0809879017522,0.0814342697949,0.0817411478243,0.081936433843,0.081936433843,0.082020127851,0.0824664958937,0.0819643318456,0.0818527398349,0.081936433843,0.0817690458269,0.0810436977575,0.0807926157335,0.0802625536827,0.0804857377041,0.0804578397014,0.07981618564,0.0797882876373,0.0795372056133,0.0795930016186,0.0797882876373,0.079983573656,0.0798440836427,0.0800114716587,0.0800393696614,0.0799556756534,0.0803741456934,0.0806252277174,0.0810157997548,0.0809042077442,0.0808484117388,0.0811273917655,0.0812668817789,0.0813226777842,0.0810715957602,0.0816295558136,0.0816574538163,0.0816853518189,0.081936433843,0.0820480258536,0.081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m <- 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ycorr <- 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altd  <- c(0, 39, 56, 120, 137, 480, 506, 542, 576, 597)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('06-PIF3-GSE39215/P3M-ChIP-1-GSM958269/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) : 0,39,56,120,137,480,506,542,576,597',bty='n')
dev.off()