# R script for Peak Model
#  -- generated by MACS
p <- c(0.0252352570439,0.0292528104041,0.033437761821,0.0376227132379,0.0426446549382,0.0422261597965,0.0431886986224,0.0434397957074,0.0437327423066,0.0441930869625,0.0446115821041,0.0449882277317,0.04557412093,0.04557412093,0.0446952811325,0.0451137762742,0.0444023345333,0.0440675384199,0.0437327423066,0.0436908927924,0.0439001403633,0.0436071937641,0.0428957520232,0.0429376015374,0.0432305481366,0.0431049995941,0.0436071937641,0.0439838393916,0.0441093879341,0.0436490432783,0.0433979461932,0.0438582908491,0.044318635505,0.0444441840475,0.0444860335616,0.0440675384199,0.0434816452216,0.0432723976507,0.0432723976507,0.0440675384199,0.0441093879341,0.0441930869625,0.0437745918208,0.0439419898774,0.0433142471649,0.0438164413349,0.0443604850191,0.0444441840475,0.0439001403633,0.0436908927924,0.0428120529949,0.0422680093107,0.0423935578532,0.0420169122257,0.042853902509,0.0433142471649,0.0430213005657,0.0423935578532,0.0426446549382,0.0426865044524,0.0437745918208,0.0441930869625,0.0444860335616,0.0446534316183,0.0441930869625,0.0440256889058,0.0439838393916,0.0444441840475,0.0446534316183,0.0444441840475,0.0440675384199,0.0444023345333,0.0445278830758,0.0444860335616,0.0449882277317,0.0451974753025,0.0453648733592,0.0451974753025,0.0451137762742,0.0453648733592,0.0448626791892,0.0446115821041,0.0442349364766,0.0437745918208,0.0438164413349,0.0433979461932,0.0432723976507,0.0436908927924,0.0436908927924,0.0431049995941,0.0440256889058,0.0440675384199,0.0441093879341,0.044318635505,0.044318635505,0.0441930869625,0.0438164413349,0.0438582908491,0.0439419898774,0.0439419898774,0.0441930869625,0.0439838393916,0.0441093879341,0.044820829675,0.0442349364766,0.0441930869625,0.0446534316183,0.044318635505,0.0441512374483,0.0441093879341,0.0435234947357,0.0431468491082,0.0435234947357,0.0434816452216,0.0434816452216,0.0438582908491,0.0436490432783,0.0436490432783,0.0440675384199,0.0444023345333,0.0450300772458,0.0458670675292,0.0451137762742,0.0446952811325,0.045323023845,0.0451974753025,0.0454067228734,0.0461181646142,0.0457833685009,0.0457833685009,0.0452393248167,0.0446952811325,0.0452393248167,0.0459507665576,0.0457833685009,0.0462437131567,0.0462855626709,0.0456159704442,0.0456159704442,0.04557412093,0.0458670675292,0.0457833685009,0.045825218015,0.0454485723875,0.0454067228734,0.045323023845,0.0456578199584,0.0460763151001,0.0466622082984,0.0471225529543,0.0478758442093,0.0483361888652,0.0485035869219,0.0483361888652,0.048294339351,0.0484198878935,0.0483780383794,0.0488802325494,0.048796533521,0.0485035869219,0.0477084461526,0.0470807034401,0.0465785092701,0.0473318005251,0.0470807034401,0.0477084461526,0.0476247471243,0.047541048096,0.0478758442093,0.0485872859502,0.0490057810919,0.0500938684603,0.0502194170028,0.0500101694319,0.0508890092295,0.0501357179745,0.0504286645736,0.0498427713753,0.0502194170028,0.0508890092295,0.0511401063145,0.0510564072862,0.0517259995129,0.0521444946546,0.0526048393104,0.0534418295938,0.0541532713347,0.0544043684197,0.0548647130755,0.053734776193,0.0536092276505,0.0541532713347,0.0548647130755,0.0547810140472,0.0546973150189,0.0548647130755,0.0546136159905,0.0550739606464,0.0543625189055,0.0553250577314,0.0559109509298,0.0549902616181,0.0547810140472,0.0555343053022,0.0559528004439,0.0565805431565,0.0569990382982,0.0566642421848,0.057208285869,0.056957188784,0.0565386936423,0.0582963732374,0.0585893198366,0.0585893198366,0.0590915140066,0.0585893198366,0.0591333635208,0.0606399460309,0.0611839897151,0.0618117324276,0.0624813246543,0.062648722711,0.0629835188243,0.0631927663952,0.062648722711,0.063402013966,0.0633601644519,0.0632764654235,0.063653111051,0.0641971547352,0.0652433925895,0.0659548343303,0.066373329472,0.0665825770429,0.0675869653829,0.0680891595529,0.0690098488647,0.0698049896339,0.0707256789456,0.0707256789456,0.0701397857472,0.0698886886622,0.0700979362331,0.0703071838039,0.0700979362331,0.0698049896339,0.0694283440064,0.0693027954638,0.0696794410914,0.0699723876906,0.0711441740873,0.0714371206865,0.0721485624273,0.072567057569,0.0734458973666,0.0745758342491,0.0751198779333,0.0753291255042,0.0754128245325,0.0760824167592,0.0764590623867,0.0767938585001,0.0774634507268,0.0786770866377,0.0793048293502,0.0795977759494,0.0794303778927,0.0810625089453,0.0813973050587,0.0829038875688,0.0835316302813,0.0837827273663,0.0842430720222,0.0840338244513,0.0845778681355,0.0844941691072,0.0870469894715,0.0873817855849,0.0883861739249,0.0885117224674,0.0883024748966,0.0894742612933,0.0905623486617,0.092612974856,0.0931988680543,0.0939103097952,0.0944125039652,0.0947473000786,0.0943288049369,0.0947473000786,0.0969234748154,0.0978860136413,0.0983463582971,0.0980115621838,0.0986393048963,0.100020338864,0.0996436932364,0.100313285463,0.101066576718,0.102447610686,0.102615008742,0.102782406799,0.103535698054,0.104540086394,0.105084130078,0.106297765989,0.107595100928,0.108808736839,0.110189770807,0.110775664005,0.111612654289,0.11353773194,0.114249173681,0.116090552305,0.117304188216,0.11755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m <- 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ycorr <- 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altd  <- c(274)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('DAPseq_of_N_crassa_NCU03077.1x36mers.unique.MACS-2.1.0_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) : 274',bty='n')
dev.off()