# R script for Peak Model
#  -- generated by MACS
p <- c(0.0204317281717,0.0244605196422,0.0277339127119,0.0313670193058,0.0355037248335,0.0356476102432,0.036582865406,0.0364749513487,0.0366907794632,0.0360792664722,0.036582865406,0.0359353810625,0.0362231518818,0.0358634383577,0.0346044410232,0.0350001258997,0.0342806988514,0.0341368134418,0.0342806988514,0.03381307127,0.0322663031162,0.0318706182396,0.0319785322969,0.0318706182396,0.0324461598783,0.0316188187727,0.0318706182396,0.0320504750017,0.0322303317638,0.0330576728693,0.034244727499,0.0348562404901,0.035539696186,0.0355756675384,0.0352159540142,0.0357914956529,0.0357914956529,0.0356835815956,0.0352878967191,0.0348202691377,0.0347483264328,0.0346404123756,0.0334893290983,0.0344605556135,0.0350360972521,0.0356116388908,0.0357555243004,0.0357914956529,0.0356476102432,0.0358274670053,0.0354317821287,0.035108039957,0.0353598394239,0.0346404123756,0.0338490426225,0.0334533577459,0.0331296155742,0.0330576728693,0.0330217015169,0.0330936442217,0.0333814150411,0.0341008420894,0.0344965269659,0.0350720686046,0.0362591232343,0.0364030086439,0.0366548081108,0.037194378397,0.0385972611412,0.0387051751985,0.0383094903219,0.0388490606081,0.0382375476171,0.0379138054453,0.037626034626,0.0371224356922,0.0372663211019,0.0364030086439,0.0354677534811,0.0354317821287,0.035719552948,0.0354677534811,0.0360432951198,0.0358274670053,0.0358634383577,0.0365109227012,0.0367986935205,0.0382015762647,0.0383094903219,0.0396044590088,0.0394605735992,0.0390289173702,0.0389929460178,0.0390289173702,0.039532516304,0.039964172533,0.0404318001144,0.0396404303613,0.0402159719999,0.0391728027799,0.0397123730661,0.0402519433523,0.0407195709337,0.0407555422861,0.0398562584757,0.0400001438854,0.0394605735992,0.0393886308944,0.0388850319605,0.0389929460178,0.0392807168371,0.0390648887226,0.0385253184364,0.0389569746654,0.0393526595419,0.0392087741323,0.0392447454847,0.0391728027799,0.039532516304,0.0400001438854,0.039964172533,0.0401080579427,0.0400720865902,0.0402519433523,0.0403238860571,0.0403238860571,0.0410433131054,0.0417267688013,0.0422663390876,0.0419066255634,0.0420505109731,0.0420864823255,0.0425181385545,0.0432375656028,0.0432735369552,0.0432375656028,0.04230231044,0.0417987115062,0.0418346828586,0.0419785682682,0.041870654211,0.0415828833917,0.041438997982,0.0410792844579,0.0412951125723,0.0414749693344,0.0425541099069,0.0429857661358,0.0426979953165,0.0435253364221,0.0443526775276,0.0449282191663,0.0456476462146,0.045683617567,0.0462231878532,0.0455757035097,0.0445325342897,0.0450001618711,0.0458275029766,0.0455757035097,0.0453598753952,0.0448562764614,0.044820305109,0.0451440472807,0.0444246202324,0.0452159899856,0.0468706721967,0.0474102424829,0.0467987294918,0.0466548440822,0.0462591592056,0.0464749873201,0.0468706721967,0.0466188727298,0.0468706721967,0.0473023284256,0.0465469300249,0.0464390159677,0.046295130558,0.0468347008442,0.0473382997781,0.047769956007,0.0469785862539,0.0470865003112,0.0481656408836,0.0478778700643,0.0482375835884,0.0484174403505,0.0503598933809,0.0499642085043,0.050539750143,0.0510433490768,0.0524102604686,0.0531656588693,0.0537412005079,0.0545685416135,0.054532570261,0.0540289713272,0.0529138594024,0.0533814869838,0.0532376015741,0.0534534296886,0.0521584610017,0.051151263134,0.0500721225616,0.0502160079713,0.050108093914,0.0497483803899,0.0503598933809,0.0504318360857,0.0507555782575,0.0510793204292,0.0528059453451,0.0537412005079,0.0548563124328,0.0548563124328,0.0560793384149,0.0570865362825,0.0565109946439,0.056870708168,0.0570145935777,0.0565109946439,0.0552879686618,0.0556836535383,0.0559714243576,0.0559354530052,0.0560793384149,0.0569426508728,0.057913877388,0.0579858200929,0.0581297055025,0.0591369033702,0.059820359066,0.0597843877136,0.0594246741895,0.0601800725902,0.0600721585329,0.060683671524,0.0600002158281,0.0602879866474,0.0601081298854,0.0603599293523,0.0608994996385,0.0617987834489,0.0620505829158,0.0624462677923,0.0621225256206,0.0616908693916,0.0628059813165,0.0638491505365,0.0643527494703,0.0642808067655,0.0641369213558,0.0648923197565,0.0661872884435,0.0668707441394,0.0680218274166,0.0697484523326,0.0695685955705,0.0701081658567,0.0711873064292,0.0712232777816,0.0725542178209,0.0711873064292,0.0708995356098,0.0705038507333,0.0701441372091,0.068489454998,0.0690649966367,0.068489454998,0.068309598236,0.0688491685222,0.0692808247512,0.0704319080284,0.0714031345436,0.0716189626581,0.0716189626581,0.0720865902395,0.0732376735168,0.0734535016313,0.0744606994989,0.0751441551948,0.0753599833093,0.0765830092914,0.0758995535955,0.0753240119569,0.0766189806438,0.0776261785114,0.0770146655204,0.0782736628549,0.0785254623218,0.0783815769121,0.0785974050266,0.0783815769121,0.0788492044935,0.0812592851053,0.0823024543254,0.0834175662502,0.083741308422,0.0838851938316,0.0853959906331,0.0874463577207,0.0874463577207,0.0884895269407,0.0898204669801,0.0901082377994,0.0902521232091,0.0916550059533,0.0943888287368,0.0962593390624,0.09726653693,0.0977341645114,0.100575901352,0.10053993,0.102194612211,0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m <- 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ycorr <- 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altd  <- c(229)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-10h-p300.pooled.sorted.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) : 229',bty='n')
dev.off()