# R script for Peak Model
#  -- generated by MACS
p <- c(0.0353039983216,0.0411661019824,0.0470055545471,0.0529129603999,0.0589381519523,0.0587342920878,0.0586346272651,0.0583990558661,0.0582676795089,0.0582993910434,0.0578191878069,0.0579415037256,0.0581544240286,0.0579777454793,0.057502072462,0.0579415037256,0.0579822756985,0.0580955311788,0.0581997262207,0.0583220421395,0.0585077811272,0.0583628141124,0.0581136520557,0.0581136520557,0.0585485531001,0.0581770751247,0.0582495586321,0.0581544240286,0.0583311025779,0.0582087866592,0.0581317729325,0.0584579487158,0.0586436877035,0.058824896472,0.0586346272651,0.0587025805533,0.058652748142,0.0586391574843,0.0582450284129,0.0583718745508,0.0586663387996,0.0582540888513,0.0580366383291,0.0577920064916,0.0579686850409,0.0579596246025,0.0579324432872,0.0583854652084,0.0587705338415,0.0585576135385,0.0586482179228,0.0585530833193,0.058589325073,0.0587705338415,0.058738822307,0.0588611382257,0.0589562728292,0.0581272427133,0.0582359679744,0.0580547592059,0.0579233828488,0.0581544240286,0.0579958663562,0.0580502289867,0.0578554295606,0.0576832812305,0.0576107977231,0.0584081163045,0.0582087866592,0.0585802646346,0.0586572783612,0.058503250908,0.0587524129646,0.0587660036223,0.0587433525262,0.0589562728292,0.0590559376519,0.0586935201149,0.058675399238,0.0586980503341,0.0587886547183,0.0585666739769,0.0586255668267,0.0585576135385,0.0584307674006,0.0580955311788,0.0580592894252,0.0582359679744,0.058290330605,0.0584262371813,0.0581861355631,0.0585712041961,0.0583175119203,0.0580366383291,0.0581317729325,0.0582676795089,0.0581181822749,0.0579868059178,0.0579641548217,0.0577376438611,0.0581136520557,0.0580275778907,0.0581363031518,0.0584081163045,0.0585440228809,0.0584896602503,0.0587524129646,0.058675399238,0.0584443580582,0.0584443580582,0.0583899954276,0.0586799294572,0.0587795942799,0.0589562728292,0.059015165679,0.059187314009,0.05912389094,0.0593322810238,0.0596765776839,0.0596720474647,0.0597354705337,0.0593096299278,0.0593775832159,0.059250737078,0.0592099651051,0.0591556024745,0.0592190255435,0.0593504019007,0.059336811243,0.0590242261174,0.0587116409917,0.0590831189671,0.0591737233514,0.0593232205854,0.0595769128613,0.0596720474647,0.05969922878,0.0597354705337,0.0598034238219,0.0600525858786,0.0603968825387,0.0602836270584,0.06027456662,0.0604648358269,0.0603787616619,0.0603017479353,0.060125069386,0.0598034238219,0.0594998991347,0.0597309403145,0.0597671820682,0.0600072836864,0.0599212095214,0.05969922878,0.0594545969425,0.0593458716815,0.0593775832159,0.0595769128613,0.0599166793022,0.059975572152,0.0599212095214,0.0596222150534,0.0595769128613,0.0595723826421,0.0597535914106,0.0601794320165,0.060573561088,0.0608181929255,0.0608861462136,0.0607366489796,0.0603198688121,0.0604965473614,0.0605237286767,0.0604014127579,0.0603651710042,0.0600933578515,0.0598894979869,0.0595316106692,0.0597490611913,0.0598804375485,0.0603697012234,0.0601884924549,0.0603651710042,0.0606007424033,0.060723058322,0.0607004072259,0.060723058322,0.0608453742407,0.0604557753885,0.0606098028417,0.0603832918811,0.0606551050338,0.0606505748146,0.0609495692826,0.0608997368713,0.0608363138023,0.0608317835831,0.0608770857752,0.0613074566004,0.0611262478319,0.0614116516423,0.0611987313393,0.0614252422999,0.061108126955,0.0611579593664,0.0614252422999,0.0616155115068,0.0617559483024,0.0612893357235,0.0612621544083,0.0610265830092,0.0613754098886,0.0614886653689,0.0616970554526,0.0617967202753,0.0616517532605,0.0618148411522,0.0617514180832,0.0618374922482,0.0620005801399,0.0622089702236,0.0619779290438,0.061746887864,0.0618239015906,0.0617740691793,0.061832962029,0.0614297725191,0.0616245719452,0.0619326268517,0.0617876598369,0.0619009153172,0.0624354811843,0.0624128300882,0.0621410169355,0.0624218905266,0.0627254152138,0.0630787723124,0.0629926981474,0.0629338052976,0.0631104838469,0.0632690415193,0.062856791571,0.0627888382828,0.0632237393272,0.0630606514356,0.0631467256006,0.0629338052976,0.0631014234085,0.0629519261745,0.0632871623962,0.0629655168321,0.0633369948075,0.0633822969996,0.0630153492434,0.0635227337952,0.0633641761228,0.0637220634406,0.0637628354135,0.0641026018544,0.0640663601007,0.0643155221574,0.0641071320736,0.0645329726796,0.0647685440786,0.0645601539948,0.0646326375022,0.0647594836402,0.0648953902165,0.0651943846846,0.0652215659998,0.0655069698102,0.0659101593201,0.0658331455935,0.066100428527,0.066376771899,0.0663359999261,0.0664039532143,0.0666938872438,0.0666893570246,0.0668841564508,0.0668297938202,0.0668750960123,0.0670789558769,0.0672420437685,0.0674413734139,0.0679714090617,0.0684153705445,0.0684516122982,0.0686735930396,0.0689182248771,0.0692715819757,0.0691492660569,0.0693984281136,0.0695977577589,0.0699556450767,0.0700643703378,0.0701730955989,0.0704086669979,0.0708345076039,0.0715729333355,0.0720667272297,0.0728912271263,0.074336367055,0.0758992926833,0.0769865452942,0.0787442703486,0.0806333717602,0.0825451242678,0.0841307009921,0.0857026870588,0.0871432967683,0.0884842416551,0.0892906206749,0.0893631041823,0.09011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m <- 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ycorr <- 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altd  <- c(162)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.unique.dedup.pseudoRep1.MACS-2.1.0.p1e-1_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) : 162',bty='n')
dev.off()