> t=read.table("/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-clusters-2hrep3.txt3.csv",sep=",",header=T) > b=read.table("/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-clusters-IGG.txt3.csv",sep=",",header=T) > summary(t) Chromosome Strand ClusterStart ClusterEnd ENSMUST00000099981: 426 -:246290 Min. : 1 Min. : 16 ENSMUST00000011934: 388 +:268101 1st Qu.: 635 1st Qu.: 672 ENSMUST00000111882: 314 Median : 1487 Median : 1523 ENSMUST00000111865: 309 Mean : 2258 Mean : 2293 ENSMUST00000111846: 260 3rd Qu.: 2846 3rd Qu.: 2881 ENSMUST00000056571: 210 Max. :106466 Max. :106489 (Other) :512484 ClusterID ClusterSequence G102160.1: 10 AATGAGGGTAAAGGTCGCTGCCAGCAGCCTCCCGT : 10 G12504.1 : 10 AATGCAGATAAAGGGGATGATGAGAAGAATACA : 10 G14409.1 : 10 ACCGAGGCATGCATCAGTCTATAGAGGAATTTCGGGCC: 10 G4112.1 : 10 ACGATCTTTTCCTTCCCTCGCATGTCCTCAG : 10 G4164.1 : 10 ACTTTGCCTTGGCCACTTCTGTCCAAAAGCATCAG : 10 G42299.1 : 10 AGATTCTGTATTGCGATCAAAAGCTTTG : 10 (Other) :514331 (Other) :514331 ReadCount ModeLocation ModeScore ConversionLocationCount Min. : 2 Min. : 1 Min. : 0.5000 Min. : 1.000 1st Qu.: 11 1st Qu.: 653 1st Qu.: 0.7757 1st Qu.: 1.000 Median : 19 Median : 1505 Median : 0.8593 Median : 2.000 Mean : 127 Mean : 2275 Mean : 0.8477 Mean : 3.457 3rd Qu.: 43 3rd Qu.: 2863 3rd Qu.: 0.9325 3rd Qu.: 4.000 Max. :926205 Max. :106470 Max. :36.7897 Max. :66.000 ConversionEventCount NonConversionEventCount Min. : 1.00 Min. : -27 1st Qu.: 2.00 1st Qu.: 45 Median : 4.00 Median : 92 Mean : 16.11 Mean : 733 3rd Qu.: 8.00 3rd Qu.: 229 Max. :315144.00 Max. :6055177 > summary(b) Chromosome Strand ClusterStart ClusterEnd ENSMUST00000099981: 219 -:117324 Min. : 1 Min. : 17 ENSMUST00000011934: 190 +:135216 1st Qu.: 687 1st Qu.: 722 ENSMUST00000111882: 171 Median : 1577 Median : 1612 ENSMUST00000111865: 157 Mean : 2367 Mean : 2402 ENSMUST00000111846: 143 3rd Qu.: 2986 3rd Qu.: 3021 ENSMUST00000047441: 79 Max. :106342 Max. :106363 (Other) :251581 ClusterID ClusterSequence G11404.1: 10 AATGATGAATGTGTGCTGGAAGATAATTCTCAGA : 10 G19405.1: 10 ACGCGTTCTCTGCCATGTCTAACACTTCCG : 10 G27432.1: 10 CACACAGGTGATATTTACACTTCCACCTGGCATGATTTCA : 10 G45330.1: 10 CACAGGTTACTCTAAATGTGACTTTTAAAAATGAAACTCA : 10 G9953.1 : 10 CACGGGGGCATGATGATTCTCTCGGCCACAGTCCTCTATAGCCTGCAT: 10 G11646.1: 9 CAGGAATTAATGCAACTGGAAGGATACACAGTGGATTAC : 10 (Other) :252481 (Other) :252480 ReadCount ModeLocation ModeScore ConversionLocationCount Min. : 2.0 Min. : 1 Min. : 0.5000 Min. : 1.000 1st Qu.: 11.0 1st Qu.: 705 1st Qu.: 0.7741 1st Qu.: 1.000 Median : 19.0 Median : 1594 Median : 0.8554 Median : 2.000 Mean : 137.9 Mean : 2384 Mean : 0.8468 Mean : 3.428 3rd Qu.: 47.0 3rd Qu.: 3004 3rd Qu.: 0.9302 3rd Qu.: 4.000 Max. :219441.0 Max. :106347 Max. :10.5884 Max. :58.000 ConversionEventCount NonConversionEventCount Min. : 1.00 Min. : -28.0 1st Qu.: 2.00 1st Qu.: 46.0 Median : 4.00 Median : 96.0 Mean : 17.61 Mean : 783.6 3rd Qu.: 9.00 3rd Qu.: 253.0 Max. :77206.00 Max. :2019166.0 > require(plotrix) Loading required package: plotrix Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘plotrix’ > > p1=hist(t$ModeScore) > p1=hist(log2(t$ModeScore)) > p1=hist(log2(t$ModeScore),breaks=50) > p1=hist((t$ModeScore),breaks=50) > p1=hist(log2(t$ModeScore),breaks=50) > p2=hist(log2(b$ModeScore),breaks=50) > plot( p1$density, col=rgb(0,0,1,1/4), xlim=c(0,10)) # first histogram > plot( p2$density, col=rgb(1,0,0,1/4), xlim=c(0,10), add=T) # second Warning messages: 1: In plot.window(...) : "add" is not a graphical parameter 2: In plot.xy(xy, type, ...) : "add" is not a graphical parameter 3: In axis(side = side, at = at, labels = labels, ...) : "add" is not a graphical parameter 4: In axis(side = side, at = at, labels = labels, ...) : "add" is not a graphical parameter 5: In box(...) : "add" is not a graphical parameter 6: In title(...) : "add" is not a graphical parameter > > plot( p1$density, col=rgb(0,0,1,1/4), xlim=c(0,10)) # first histogram > points( p2$density, col=rgb(1,0,0,1/4), xlim=c(0,10), add=T) # second Warning message: In plot.xy(xy.coords(x, y), type = type, ...) : "add" is not a graphical parameter > plot( p1$density, col=rgb(0,0,1,1/4), xlim=c(0,20)) # first histogram > plot( p1$density, col=rgb(0,0,1,1/4), xlim=c(0,11)) # first histogram > plot( p1$density, col=rgb(0,0,1,1/4), xlim=c(0,10)) # first histogram > points( p2$density, col=rgb(1,0,0,1/4), xlim=c(0,10), add=T) # second Warning message: In plot.xy(xy.coords(x, y), type = type, ...) : "add" is not a graphical parameter > plot( p1$density, col=rgb(0,0,1,1/4), xlim=c(0,10)) # first histogram > points( p2$density, col=rgb(1,0,0,1/4), xlim=c(0,10)) # second > p1=hist(ModeLocation) Error in hist(ModeLocation) : object 'ModeLocation' not found > p1=hist(t$ModeLocation) > p1=hist(log2(t$ModeLocation)) > p2=hist(log2(b$ModeLocation)) > p1=hist(log2(t$ModeLocation)) > p2=hist(log2(b$ModeLocation)) > q()