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1 INFO @ Wed, 17 Sep 2014 07:06:29:
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2 # ARGUMENTS:
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3 # name = ceas_out
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4 # gene annotation table = /panfs/roc/rissdb/galaxy/libdata/cistrome/ceasdb/mm9.refGene.ceasdb
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5 # BED file = /panfs/roc/galaxy/NEXTGEN/database/files/008/dataset_8899.dat
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6 # WIG file = /panfs/roc/galaxy/NEXTGEN/database/files/008/dataset_8900.dat
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7 # extra BED file = None
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8 # ChIP annotation = On
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9 # gene-centered annotation = On
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10 # average profiling = On
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11 # dump profiles = Off
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12 # re-annotation for genome background (ChIP region annotation) = False
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13 # promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
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14 # downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
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15 # bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
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16 # span size (gene-centered annotation) = 3000 bp
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17 # profiling resolution (average profiling) = 50 bp
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18 # relative distance wrt TSS and TTS (average profiling) = 3000 bp
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19 INFO @ Wed, 17 Sep 2014 07:06:29: #1 read the gene table...
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20 INFO @ Wed, 17 Sep 2014 07:06:32: #2 read the bed file of ChIP regions...
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21 INFO @ Wed, 17 Sep 2014 07:06:32: #3 perform gene-centered annotation...
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22 INFO @ Wed, 17 Sep 2014 07:06:32: #4 See ceas_out.xls for gene-centered annotation!
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23 INFO @ Wed, 17 Sep 2014 07:06:32: #5 read the pre-computed genome bg annotation...
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24 INFO @ Wed, 17 Sep 2014 07:06:32: #6 perform ChIP region annotation...
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25 INFO @ Wed, 17 Sep 2014 07:06:32: #7 write a R script of ChIP region annotation...
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26 INFO @ Wed, 17 Sep 2014 07:06:32: #8-1 run wig profiling of chr19...
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27 INFO @ Wed, 17 Sep 2014 07:06:56: #9 append an R script of wig profiling...
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28
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29 R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
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30 Copyright (C) 2012 The R Foundation for Statistical Computing
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31 ISBN 3-900051-07-0
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32 Platform: x86_64-unknown-linux-gnu (64-bit)
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33
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34 R is free software and comes with ABSOLUTELY NO WARRANTY.
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35 You are welcome to redistribute it under certain conditions.
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36 Type 'license()' or 'licence()' for distribution details.
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37
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38 Natural language support but running in an English locale
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39
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40 R is a collaborative project with many contributors.
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41 Type 'contributors()' for more information and
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42 'citation()' on how to cite R or R packages in publications.
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43
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44 Type 'demo()' for some demos, 'help()' for on-line help, or
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45 'help.start()' for an HTML browser interface to help.
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46 Type 'q()' to quit R.
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47
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48 > # ARGUMENTS:
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49 > # name = ceas_out
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50 > # gene annotation table = /panfs/roc/rissdb/galaxy/libdata/cistrome/ceasdb/mm9.refGene.ceasdb
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51 > # BED file = /panfs/roc/galaxy/NEXTGEN/database/files/008/dataset_8899.dat
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52 > # WIG file = /panfs/roc/galaxy/NEXTGEN/database/files/008/dataset_8900.dat
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53 > # extra BED file = None
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54 > # ChIP annotation = On
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55 > # gene-centered annotation = On
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56 > # average profiling = On
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57 > # dump profiles = Off
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58 > # re-annotation for genome background (ChIP region annotation) = False
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59 > # promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
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60 > # downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
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61 > # bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
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62 > # span size (gene-centered annotation) = 3000 bp
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63 > # profiling resolution (average profiling) = 50 bp
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64 > # relative distance wrt TSS and TTS (average profiling) = 3000 bp
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65 > pdf("ceas_out.pdf",height=11.5,width=8.5)
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66 >
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67 > # 07:06:32 Wed, 17 Sep 2014
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68 > #
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69 > # ChIP annotation
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70 > #
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71 >
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72 >
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73 > #
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74 > # Chromosomal Distribution
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75 > #
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76 >
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77 > par(mar=c(4, 4, 5, 3.7999999999999998),oma=c(4, 2, 4, 2))
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78 > r0<-c(0.045979148030396322, 4.8040981077812157, 2.4433812358090048, 3.5802744033489131, 3.5571041139849155, 3.8595377043212911, 4.1146432356308704, 4.5518259349760362, 4.5475016748440362, 4.5167865196676384, 5.1251711955223902, 5.0836389358963929, 4.9285399877888052, 5.1167227529659911, 5.1322836353215893, 5.7783410072815382, 5.87459129287633, 5.9537123450527236, 6.0221647375303178, 7.4772653637090016, 7.4864366676606009)
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79 > r1<-c(0.0, 0.0, 100.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
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80 > height<-rbind(r0,r1)
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81 > names=c("Y","X","19","18","17","16","15","14","13","12","11","10","9","8","7","6","5","4","3","2","1")
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82 > mp<-barplot(height=height,names=names,beside=TRUE,horiz=TRUE,col=c("#5FA1C1","#EB9D86"),main="Chromosomal Distribution of ChIP Regions",xlab="Percentage %",ylab="Chromosome",border=FALSE,xlim=c(0.000000,183.333333),cex.names=0.833333333333)
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83 > text(x=c(0.045979148030396322, 4.8040981077812157, 2.4433812358090048, 3.5802744033489131, 3.5571041139849155, 3.8595377043212911, 4.1146432356308704, 4.5518259349760362, 4.5475016748440362, 4.5167865196676384, 5.1251711955223902, 5.0836389358963929, 4.9285399877888052, 5.1167227529659911, 5.1322836353215893, 5.7783410072815382, 5.87459129287633, 5.9537123450527236, 6.0221647375303178, 7.4772653637090016, 7.4864366676606009),y=mp[1,],label=c("0.05 %","4.8 %","2.4 %","3.6 %","3.6 %","3.9 %","4.1 %","4.6 %","4.5 %","4.5 %","5.1 %","5.1 %","4.9 %","5.1 %","5.1 %","5.8 %","5.9 %","6.0 %","6.0 %","7.5 %","7.5 %"),pos=4,offset=0.2,cex=0.733333333333)
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84 > text(x=c(0.0, 0.0, 100.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0),y=mp[2,],label=c("0.000 % (0.726)","0.000 % (1.4e-15)","100.0 % (<=4.9e-324)","0.000 % (9.9e-12)","0.000 % (1.2e-11)","0.000 % (1.3e-12)","0.000 % (2.1e-13)","0.000 % (8.7e-15)","0.000 % (9.0e-15)","0.000 % (1.1e-14)","0.000 % (1.3e-16)","0.000 % (1.8e-16)","0.000 % (5.6e-16)","0.000 % (1.4e-16)","0.000 % (1.3e-16)","0.000 % (1.1e-18)","0.000 % (5.3e-19)","0.000 % (3.0e-19)","0.000 % (1.8e-19)","0.000 % (3.5e-24)","0.000 % (3.3e-24)"),pos=4,offset=0.2,cex=0.733333333333)
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85 > legend("right",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
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86 >
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87 > #
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88 > # Promoter,Bipromoter,Downstream, Gene and Regions of interest
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89 > #
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90 >
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91 > par(mfrow=c(4, 1),mar=c(4, 4, 5, 3.7999999999999998),oma=c(4, 2, 4, 2))
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92 > r0<-c(1.1190475268459104, 1.9804336910206417, 2.7300861366801819)
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93 > r1<-c(11.798561151079138, 14.820143884892087, 16.115107913669064)
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94 > height<-rbind(r0,r1)
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95 > names=c("<=1000 bp","<=2000 bp","<=3000 bp")
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96 > mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Promoter",ylab="Percentage %",border=FALSE,ylim=c(0.000000,29.544365),cex.names=1)
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97 > text(x=mp[1,],y=c(1.1190475268459104, 1.9804336910206417, 2.7300861366801819),label=c("1.1 %","2.0 %","2.7 %"),pos=3,offset=0.2)
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98 > text(x=mp[2,],y=c(11.798561151079138, 14.820143884892087, 16.115107913669064),label=c("11.8 %
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99 + (1.5e-56)","14.8 %
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100 + (6.4e-57)","16.1 %
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101 + (9.3e-52)"),pos=3,offset=0.2)
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102 > legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
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103 > r0<-c(0.032151196787397432, 0.075235672177193971)
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104 > r1<-c(1.5827338129496402, 1.8705035971223021)
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105 > height<-rbind(r0,r1)
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106 > names=c("<=2500 bp","<=5000 bp")
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107 > mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Bidirectional Promoter",ylab="Percentage %",border=FALSE,ylim=c(0.000000,3.429257),cex.names=1)
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108 > text(x=mp[1,],y=c(0.032151196787397432, 0.075235672177193971),label=c("0.03 %","0.08 %"),pos=3,offset=0.2)
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109 > text(x=mp[2,],y=c(1.5827338129496402, 1.8705035971223021),label=c("1.6 %
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110 + (2.4e-17)","1.9 %
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111 + (7.1e-16)"),pos=3,offset=0.2)
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112 > legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
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113 > r0<-c(1.0253272561343179, 1.847130304802252, 2.5592843155857952)
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114 > r1<-c(2.5899280575539567, 4.1726618705035978, 5.755395683453238)
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115 > height<-rbind(r0,r1)
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116 > names=c("<=1000 bp","<=2000 bp","<=3000 bp")
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117 > mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Downstream",ylab="Percentage %",border=FALSE,ylim=c(0.000000,10.551559),cex.names=1)
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118 > text(x=mp[1,],y=c(1.0253272561343179, 1.847130304802252, 2.5592843155857952),label=c("1.0 %","1.8 %","2.6 %"),pos=3,offset=0.2)
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119 > text(x=mp[2,],y=c(2.5899280575539567, 4.1726618705035978, 5.755395683453238),label=c("2.6 %
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120 + (1.5e-04)","4.2 %
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121 + (2.5e-05)","5.8 %
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122 + (1.2e-06)"),pos=3,offset=0.2)
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123 > legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
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124 > r0<-c(0.29665715329437625, 1.3393201746742929, 2.063711196219435, 39.842674380630413, 43.542362904818518)
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125 > r1<-c(4.1726618705035978, 1.1510791366906474, 1.7266187050359711, 45.323741007194243, 52.374100719424469)
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126 > height<-rbind(r0,r1)
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127 > names=c("5'UTR","3'UTR","Coding Exon","Intron","All")
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128 > mp<-barplot(height=height,names=names,beside=TRUE,horiz=FALSE,col=c("#5FA1C1","#EB9D86"),main="Gene",ylab="Percentage %",border=FALSE,ylim=c(0.000000,96.019185),cex.names=1)
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129 > text(x=mp[1,],y=c(0.29665715329437625, 1.3393201746742929, 2.063711196219435, 39.842674380630413, 43.542362904818518),label=c("0.3 %","1.3 %","2.1 %","39.8 %","43.5 %"),pos=3,offset=0.2)
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130 > text(x=mp[2,],y=c(4.1726618705035978, 1.1510791366906474, 1.7266187050359711, 45.323741007194243, 52.374100719424469),label=c("4.2 %
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131 + (7.9e-25)","1.2 %
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132 + (0.415)","1.7 %
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133 + (0.323)","45.3 %
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134 + (0.001)","52.4 %
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135 + (1.2e-06)"),pos=3,offset=0.2)
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136 > legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
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137 >
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138 > #
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139 > # Distribution of Genome and ChIP regions over cis-regulatory element
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140 > # Note that the x may be modified for better graphics in case a value is too small
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141 > # Thus, look at the labels of the pie chart to get the real percentage values
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142 > #
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143 >
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144 > par(mfcol=c(2, 2),mar=c(3, 3, 4, 2.7999999999999998),oma=c(4, 2, 4, 2))
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145 > x<-c(0.011190,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.012749,0.020109,0.392862,0.520644)
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146 > pie(x=x,labels=c("1.1 %","0.8 %","0.7 %","1.0 %","0.8 %","0.7 %","0.3 %","1.3 %","2.0 %","39.3 %","52.1 %"),main="Genome",col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),clockwise=TRUE,border=FALSE,radius=0.9,cex=0.8,init.angle=90,density=100)
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147 > x<-c(0.000000,1.000000)
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148 > y<-c(0.000000,1.000000)
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149 > plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
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150 > legend("top",legend=c("Promoter (<=1000 bp): 1.1 %","Promoter (1000-2000 bp): 0.8 %","Promoter (2000-3000 bp): 0.7 %","Downstream (<=1000 bp): 1.0 %","Downstream (1000-2000 bp): 0.8 %","Downstream (2000-3000 bp): 0.7 %","5'UTR: 0.3 %","3'UTR: 1.3 %","Coding exon: 2.0 %","Intron: 39.3 %","Distal intergenic: 52.1 %"),col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),pch=15,bty="n")
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151 > x<-c(0.117986,0.027338,0.011511,0.023022,0.015827,0.010072,0.037410,0.010000,0.015827,0.440288,0.292086)
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152 > pie(x=x,labels=c("11.8 %","2.7 %","1.2 %","2.3 %","1.6 %","1.0 %","3.7 %","0.9 %","1.6 %","44.0 %","29.2 %"),main="ChIP",col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),clockwise=TRUE,border=FALSE,radius=0.9,cex=0.8,init.angle=90,density=100)
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153 > x<-c(0.000000,1.000000)
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154 > y<-c(0.000000,1.000000)
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155 > plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
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156 > legend("top",legend=c("Promoter (<=1000 bp): 11.8 %","Promoter (1000-2000 bp): 2.7 %","Promoter (2000-3000 bp): 1.2 %","Downstream (<=1000 bp): 2.3 %","Downstream (1000-2000 bp): 1.6 %","Downstream (2000-3000 bp): 1.0 %","5'UTR: 3.7 %","3'UTR: 0.9 %","Coding exon: 1.6 %","Intron: 44.0 %","Distal intergenic: 29.2 %"),col=c("#445FA2","#EB9D86","#799F7A","#6C527F","#5FA1C1","#E8BB77","#A8C5EF","#FDCDB9","#C6E6B5","#F1D5EE","#B4E1F6"),pch=15,bty="n")
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157 >
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158 > #
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159 > # ChIP regions over the genome
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160 > #
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161 >
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162 > par(mar=c(4, 4, 5, 3.7999999999999998),oma=c(4, 2, 4, 2))
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163 > layout(matrix(c(1, 0, 2, 2), 2, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 5))
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164 > x<-c(0.000000,6.000000)
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165 > y<-c(0.000000,1.000000)
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166 > plot(x, y,type="n",main="Distribution of Peak Heights",xlab="",ylab="",xlim=c(0.000000,6.000000),ylim=c(0.000000,1.000000),frame=FALSE,xaxt="s",yaxt="n",cex=0.9)
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167 > x<-c(0.000000,6.000000,6.000000,0.000000)
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168 > y<-c(0.000000,0.000000,1.000000,1.000000)
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169 > polygon(x,y,col=c("black"))
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170 > x <- c(0.000000,0.387500,0.775000,1.162500,1.550000,1.937500,2.325000,2.712500,3.100000,3.487500,3.875000,4.262500,4.650000,5.037500,5.425000,5.812500)
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171 > y<-c(0.192000,0.000000,0.448000,0.000000,0.000000,0.656000,0.000000,0.800000,0.000000,0.000000,0.464000,0.000000,0.240000,0.000000,0.000000,0.096000)
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172 > lines(x, y,xlim=c(0, 6.0),ylim=c(0, 1),type="l",col=c("cyan"),lwd=2)
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173 > x<-c(3084201.000000,61342311.000000)
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174 > y<-c(0.855556,1.144444)
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175 > plot(x, y,type="n",main="ChIP Regions (Peaks) over Chromosomes",xlab="Chromosome Size (bp)",ylab="Chromosome",xlim=c(3084201.000000,61342311.000000),ylim=c(0.855556,1.144444),frame=FALSE,xaxt="s",yaxt="n")
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176 > start <- c(3320108, 3609773, 3767725, 3985110, 4125778, 4326039, 4462134, 4578749, 4701240, 4836062, 5118390, 5273183, 5488268, 5663088, 5790466, 5929626, 6061998, 6235653, 6401146, 6546368, 6983941, 7132411, 7381367, 7557560, 7877082, 8326707, 8704813, 8955294, 9154056, 9999162, 10130532, 10257335, 10679795, 11127807, 12051913, 12519522, 12675546, 12806385, 14301025, 14799146, 15979223, 16635529, 17357824, 17483150, 17627897, 17837233, 18250701, 18379283, 18643061, 18787433, 20525706, 20705523, 20904857, 21029400, 21180751, 21346321, 21546970, 21698703, 21889000, 22991270, 23109335, 23239277, 23363849, 23560771, 24248702, 24757808, 25036212, 25164340, 25449550, 26679300, 26828832, 27402068, 28731385, 28886972, 29119945, 29477771, 29722786, 30186029, 30304057, 31943035, 32226625, 32396979, 32582044, 32701167, 32830073, 33172241, 34170778, 34364534, 34570847, 34760029, 34878860, 36248548, 36484016, 36628380, 36762687, 36883927, 37281882, 37508826, 37625125, 37769605, 37941974, 38129309, 38265937, 38444821, 38589096, 38757848, 38910914, 39079754, 39349984, 39576660, 40261604, 40379114, 40551911, 40924308, 41068591, 41337913, 41459429, 41648180, 41903460, 42127635, 42317120, 42584793, 42729654, 42854351, 43136857, 43586812, 43854832, 43970453, 44096027, 44322511, 44454629, 44617369, 45063231, 45235617, 45619624, 46164946, 46365158, 46529633, 46647839, 46781407, 46980553, 47224264, 47354328, 47477521, 47653727, 47929969, 48774816, 49092263, 49497948, 53217226, 53464973, 53628909, 53855083, 53977537, 54273888, 55170177, 55306583, 55624627, 55775858, 55913805, 56352889, 56471407, 56593906, 56758930, 56947282, 57194791, 57332280, 57451609, 57626327, 58000191, 58117871, 58449187, 58700784, 58945367, 59145950, 59441860, 59731304, 60386876, 60656761, 60866506, 61021828, 61275501)
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177 > end <- c(3320504, 3610400, 3767975, 3985808, 4125968, 4326483, 4462297, 4579283, 4701513, 4836384, 5118559, 5273392, 5488625, 5663367, 5790611, 5929806, 6062229, 6236101, 6401769, 6546543, 6984290, 7132701, 7381770, 7557889, 7877388, 8326801, 8705147, 8955548, 9154376, 9999448, 10130836, 10257564, 10680183, 11128083, 12052090, 12519773, 12676153, 12806600, 14301365, 14799437, 15979481, 16635760, 17358126, 17483438, 17628217, 17837627, 18251001, 18379703, 18643939, 18787673, 20526019, 20705904, 20905034, 21029752, 21181208, 21346940, 21547232, 21698959, 21889329, 22991525, 23109858, 23239657, 23364016, 23561025, 24248904, 24758083, 25036433, 25164509, 25449962, 26679689, 26829062, 27402407, 28731696, 28887111, 29120264, 29478060, 29723009, 30186408, 30304420, 31943349, 32226779, 32397237, 32582437, 32702099, 32830275, 33172586, 34171142, 34364977, 34571203, 34760394, 34879388, 36248712, 36484269, 36628954, 36763023, 36884286, 37282254, 37509600, 37625585, 37769978, 37942448, 38129608, 38266386, 38445076, 38589541, 38758081, 38911164, 39079988, 39350093, 39576847, 40261988, 40379330, 40552118, 40924449, 41068813, 41338181, 41459703, 41648476, 41903928, 42127874, 42317305, 42585224, 42729814, 42854547, 43137011, 43587193, 43855294, 43970798, 44096434, 44322733, 44455079, 44617517, 45063524, 45235846, 45619769, 46165116, 46365482, 46529858, 46648067, 46781663, 46980800, 47224654, 47354952, 47477977, 47653937, 47930187, 48775162, 49092447, 49498374, 53217430, 53465487, 53629180, 53855670, 53977996, 54274304, 55170416, 55306996, 55625075, 55776152, 55914000, 56353213, 56471926, 56594369, 56759295, 56947684, 57194965, 57332779, 57452025, 57626516, 58000629, 58118405, 58449559, 58700919, 58945518, 59146259, 59442090, 59731501, 60387098, 60657160, 60866799, 61022265, 61275794)
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178 > vals <- c(4.0, 3.0, 0.0, 3.0, 2.0, 5.0, 2.0, 4.0, 3.0, 5.0, 2.0, 1.0, 4.0, 2.0, 1.0, 1.0, 3.0, 5.0, 2.0, 1.0, 3.0, 1.0, 3.0, 2.0, 3.0, 1.0, 3.0, 4.0, 3.0, 3.0, 5.0, 0.0, 5.0, 2.0, 1.0, 4.0, 5.0, 1.0, 2.0, 2.0, 2.0, 0.0, 2.0, 0.0, 3.0, 5.0, 3.0, 4.0, 2.0, 1.0, 2.0, 4.0, 2.0, 4.0, 6.0, 3.0, 2.0, 3.0, 5.0, 4.0, 4.0, 3.0, 4.0, 1.0, 2.0, 0.0, 2.0, 5.0, 2.0, 4.0, 3.0, 4.0, 1.0, 0.0, 3.0, 3.0, 1.0, 1.0, 4.0, 4.0, 1.0, 3.0, 2.0, 4.0, 3.0, 3.0, 3.0, 2.0, 2.0, 3.0, 2.0, 1.0, 2.0, 3.0, 3.0, 3.0, 3.0, 4.0, 6.0, 3.0, 5.0, 2.0, 6.0, 3.0, 4.0, 4.0, 2.0, 3.0, 0.0, 2.0, 4.0, 1.0, 3.0, 0.0, 1.0, 4.0, 3.0, 2.0, 4.0, 2.0, 1.0, 4.0, 2.0, 4.0, 0.0, 3.0, 3.0, 3.0, 4.0, 1.0, 3.0, 1.0, 2.0, 3.0, 1.0, 2.0, 5.0, 2.0, 3.0, 4.0, 5.0, 3.0, 2.0, 2.0, 3.0, 1.0, 1.0, 0.0, 4.0, 2.0, 2.0, 3.0, 2.0, 2.0, 3.0, 3.0, 1.0, 3.0, 6.0, 1.0, 5.0, 3.0, 6.0, 3.0, 1.0, 3.0, 2.0, 5.0, 0.0, 6.0, 5.0, 3.0, 1.0, 0.0, 3.0, 4.0, 2.0, 2.0, 3.0, 1.0, 4.0, 21.0)
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179 > vals[vals > 6.0] <- 6.0
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180 > vals[vals < 0] <- 0
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181 > heights <- 0.288889 * ((vals - 0)/(6.0 - 0)) + 0.855555555556
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182 > for (i in 1:length(heights)) {
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183 + polygon(x=c(start[i], end[i], end[i], start[i]), y=c(0.855555555556, 0.855555555556, heights[i], heights[i]), col=c("#CC0000"), border=c("#CC0000"))
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184 + }
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185 > mtext("19",side=2,line=0,outer=FALSE,at=1.0)
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186 > par(mar=c(4, 4, 5, 3.7999999999999998),oma=c(4, 2, 4, 2))
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187 > layout(matrix(c(1, 2, 3, 3, 4, 5), 3, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 1, 1))
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188 > x<-c(-3000.000000,-2950.000000,-2900.000000,-2850.000000,-2800.000000,-2750.000000,-2700.000000,-2650.000000,-2600.000000,-2550.000000,-2500.000000,-2450.000000,-2400.000000,-2350.000000,-2300.000000,-2250.000000,-2200.000000,-2150.000000,-2100.000000,-2050.000000,-2000.000000,-1950.000000,-1900.000000,-1850.000000,-1800.000000,-1750.000000,-1700.000000,-1650.000000,-1600.000000,-1550.000000,-1500.000000,-1450.000000,-1400.000000,-1350.000000,-1300.000000,-1250.000000,-1200.000000,-1150.000000,-1100.000000,-1050.000000,-1000.000000,-950.000000,-900.000000,-850.000000,-800.000000,-750.000000,-700.000000,-650.000000,-600.000000,-550.000000,-500.000000,-450.000000,-400.000000,-350.000000,-300.000000,-250.000000,-200.000000,-150.000000,-100.000000,-50.000000,0.000000,50.000000,100.000000,150.000000,200.000000,250.000000,300.000000,350.000000,400.000000,450.000000,500.000000,550.000000,600.000000,650.000000,700.000000,750.000000,800.000000,850.000000,900.000000,950.000000,1000.000000,1050.000000,1100.000000,1150.000000,1200.000000,1250.000000,1300.000000,1350.000000,1400.000000,1450.000000,1500.000000,1550.000000,1600.000000,1650.000000,1700.000000,1750.000000,1800.000000,1850.000000,1900.000000,1950.000000,2000.000000,2050.000000,2100.000000,2150.000000,2200.000000,2250.000000,2300.000000,2350.000000,2400.000000,2450.000000,2500.000000,2550.000000,2600.000000,2650.000000,2700.000000,2750.000000,2800.000000,2850.000000,2900.000000,2950.000000,3000.000000)
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189 > y<-c(0.542169,0.647317,0.634173,0.593647,0.562979,0.569551,0.639650,0.631982,0.595838,0.611172,0.627601,0.628697,0.659365,0.595838,0.581599,0.593647,0.583790,0.633078,0.619934,0.638554,0.604600,0.619934,0.635268,0.662651,0.651698,0.699890,0.624315,0.634173,0.650602,0.654984,0.704272,0.695509,0.671413,0.730559,0.742607,0.742607,0.760131,0.757941,0.778751,0.819277,0.856517,0.837897,0.890471,0.889376,0.875137,0.871851,0.904710,0.929901,0.930997,0.968237,0.960570,0.963855,0.946331,0.995619,1.007667,1.048193,1.060241,1.038335,1.042716,0.984666,0.980285,0.941950,0.859803,0.746988,0.721796,0.778751,0.732749,0.732749,0.807229,0.823658,0.819277,0.865279,0.836802,0.822563,0.814896,0.809419,0.849945,0.890471,0.861993,0.802848,0.811610,0.783133,0.748083,0.813801,0.757941,0.738226,0.743702,0.727273,0.719606,0.707558,0.768894,0.717415,0.746988,0.713034,0.671413,0.673604,0.673604,0.738226,0.700986,0.633078,0.681271,0.702081,0.720701,0.663746,0.726177,0.714129,0.649507,0.670318,0.677985,0.676889,0.672508,0.669222,0.646221,0.669222,0.642935,0.684556,0.696605,0.642935,0.681271,0.685652,0.623220)
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190 > plot(x, y,type="l",main="Average Profile near TSS",xlab="Relative Distance to TSS (bp)",ylab="Average Profile",col=c("#C8524D"),xaxt="s",yaxt="s",lwd=2)
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191 > abline(v=0.000000,lty=2,col=c("black"))
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192 > x<-c(-3000.000000,-2950.000000,-2900.000000,-2850.000000,-2800.000000,-2750.000000,-2700.000000,-2650.000000,-2600.000000,-2550.000000,-2500.000000,-2450.000000,-2400.000000,-2350.000000,-2300.000000,-2250.000000,-2200.000000,-2150.000000,-2100.000000,-2050.000000,-2000.000000,-1950.000000,-1900.000000,-1850.000000,-1800.000000,-1750.000000,-1700.000000,-1650.000000,-1600.000000,-1550.000000,-1500.000000,-1450.000000,-1400.000000,-1350.000000,-1300.000000,-1250.000000,-1200.000000,-1150.000000,-1100.000000,-1050.000000,-1000.000000,-950.000000,-900.000000,-850.000000,-800.000000,-750.000000,-700.000000,-650.000000,-600.000000,-550.000000,-500.000000,-450.000000,-400.000000,-350.000000,-300.000000,-250.000000,-200.000000,-150.000000,-100.000000,-50.000000,0.000000,50.000000,100.000000,150.000000,200.000000,250.000000,300.000000,350.000000,400.000000,450.000000,500.000000,550.000000,600.000000,650.000000,700.000000,750.000000,800.000000,850.000000,900.000000,950.000000,1000.000000,1050.000000,1100.000000,1150.000000,1200.000000,1250.000000,1300.000000,1350.000000,1400.000000,1450.000000,1500.000000,1550.000000,1600.000000,1650.000000,1700.000000,1750.000000,1800.000000,1850.000000,1900.000000,1950.000000,2000.000000,2050.000000,2100.000000,2150.000000,2200.000000,2250.000000,2300.000000,2350.000000,2400.000000,2450.000000,2500.000000,2550.000000,2600.000000,2650.000000,2700.000000,2750.000000,2800.000000,2850.000000,2900.000000,2950.000000,3000.000000)
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193 > y<-c(0.598028,0.580504,0.608981,0.652793,0.634173,0.630887,0.573932,0.617744,0.636364,0.572837,0.592552,0.633078,0.606791,0.611172,0.645126,0.627601,0.617744,0.575027,0.519168,0.557503,0.616648,0.661555,0.673604,0.671413,0.585980,0.558598,0.590361,0.623220,0.598028,0.566265,0.630887,0.614458,0.608981,0.619934,0.607886,0.627601,0.544359,0.581599,0.557503,0.561884,0.610077,0.604600,0.618839,0.594743,0.608981,0.581599,0.561884,0.579409,0.556407,0.529025,0.549836,0.592552,0.598028,0.595838,0.606791,0.592552,0.565170,0.602410,0.602410,0.677985,0.722892,0.752464,0.691128,0.627601,0.561884,0.602410,0.626506,0.613363,0.560789,0.562979,0.672508,0.650602,0.649507,0.641840,0.660460,0.687842,0.650602,0.669222,0.629792,0.590361,0.644031,0.644031,0.693319,0.625411,0.583790,0.592552,0.590361,0.637459,0.645126,0.619934,0.618839,0.605696,0.568456,0.598028,0.578313,0.538883,0.585980,0.618839,0.617744,0.600219,0.634173,0.653888,0.623220,0.610077,0.638554,0.611172,0.644031,0.630887,0.582694,0.612267,0.646221,0.637459,0.631982,0.677985,0.606791,0.581599,0.562979,0.601314,0.590361,0.585980,0.570646)
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194 > plot(x, y,type="l",main="Average Profile near TTS",xlab="Relative Distance to TTS (bp)",ylab="Average Profile",col=c("#C8524D"),xaxt="s",yaxt="s",lwd=2)
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195 > abline(v=0.000000,lty=2,col=c("black"))
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196 > x<-c(-1000.000000,-950.000000,-900.000000,-850.000000,-800.000000,-750.000000,-700.000000,-650.000000,-600.000000,-550.000000,-500.000000,-450.000000,-400.000000,-350.000000,-300.000000,-250.000000,-200.000000,-150.000000,-100.000000,-50.000000,0.000000,50.000000,100.000000,150.000000,200.000000,250.000000,300.000000,350.000000,400.000000,450.000000,500.000000,550.000000,600.000000,650.000000,700.000000,750.000000,800.000000,850.000000,900.000000,950.000000,1000.000000,1050.000000,1100.000000,1150.000000,1200.000000,1250.000000,1300.000000,1350.000000,1400.000000,1450.000000,1500.000000,1550.000000,1600.000000,1650.000000,1700.000000,1750.000000,1800.000000,1850.000000,1900.000000,1950.000000,2000.000000,2050.000000,2100.000000,2150.000000,2200.000000,2250.000000,2300.000000,2350.000000,2400.000000,2450.000000,2500.000000,2550.000000,2600.000000,2650.000000,2700.000000,2750.000000,2800.000000,2850.000000,2900.000000,2950.000000,3000.000000,3050.000000,3100.000000,3150.000000,3200.000000,3250.000000,3300.000000,3350.000000,3400.000000,3450.000000,3500.000000,3550.000000,3600.000000,3650.000000,3700.000000,3750.000000,3800.000000,3850.000000,3900.000000,3950.000000,4000.000000)
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197 > y<-c(0.856517,0.837897,0.890471,0.889376,0.875137,0.871851,0.904710,0.929901,0.930997,0.968237,0.960570,0.963855,0.946331,0.995619,1.007667,1.048193,1.060241,1.038335,1.042716,0.984666,0.980285,0.859375,0.895089,0.812500,0.820312,0.795759,0.787946,0.818080,0.745536,0.770089,0.704241,0.790179,0.745536,0.725446,0.712054,0.658482,0.725446,0.726562,0.694196,0.689732,0.687500,0.748884,0.710938,0.683036,0.661830,0.693080,0.670759,0.678571,0.633929,0.695312,0.690848,0.678571,0.679688,0.675223,0.660714,0.659598,0.668527,0.689732,0.708705,0.755580,0.639509,0.680804,0.684152,0.649554,0.639509,0.691964,0.685268,0.678571,0.620536,0.660714,0.676339,0.706473,0.661830,0.683036,0.748884,0.672991,0.645089,0.643973,0.700893,0.704241,0.771205,0.752464,0.691128,0.627601,0.561884,0.602410,0.626506,0.613363,0.560789,0.562979,0.672508,0.650602,0.649507,0.641840,0.660460,0.687842,0.650602,0.669222,0.629792,0.590361,0.644031)
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198 > plot(x, y,type="l",main="Average Gene Profile",xlab="Upstream (bp), 3000 bp of Meta-gene, Downstream (bp)",ylab="Average Profile",col=c("#C8524D"),xaxt="s",yaxt="s",lwd=2)
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199 > abline(v=0.000000,lty=2,col=c("black"))
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200 > abline(v=3000.000000,lty=2,col=c("black"))
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201 > x<-c(0.000000,3.333333,6.666667,10.000000,13.333333,16.666667,20.000000,23.333333,26.666667,30.000000,33.333333,36.666667,40.000000,43.333333,46.666667,50.000000,53.333333,56.666667,60.000000,63.333333,66.666667,70.000000,73.333333,76.666667,80.000000,83.333333,86.666667,90.000000,93.333333,96.666667,100.000000)
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202 > y<-c(1.005650,0.821469,0.728814,0.807910,0.753672,0.749153,0.680226,0.722034,0.714124,0.761582,0.757062,0.711864,0.672316,0.667797,0.661017,0.716384,0.751412,0.702825,0.732203,0.774011,0.724294,0.673446,0.770621,0.737853,0.707345,0.688136,0.763842,0.760452,0.734463,0.779661,0.850847)
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203 > plot(x, y,type="l",main="Average Concatenated Exon Profile",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.598504,1.005650),xaxt="s",yaxt="s",lwd=2)
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204 > x<-c(0.000000,3.333333,6.666667,10.000000,13.333333,16.666667,20.000000,23.333333,26.666667,30.000000,33.333333,36.666667,40.000000,43.333333,46.666667,50.000000,53.333333,56.666667,60.000000,63.333333,66.666667,70.000000,73.333333,76.666667,80.000000,83.333333,86.666667,90.000000,93.333333,96.666667,100.000000)
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205 > y<-c(0.901496,0.855362,0.795511,0.776808,0.721945,0.708229,0.700748,0.690773,0.628429,0.653367,0.690773,0.684539,0.644638,0.634663,0.709476,0.665835,0.598504,0.664589,0.619701,0.684539,0.652120,0.624688,0.630923,0.635910,0.674564,0.619701,0.630923,0.689526,0.699501,0.648379,0.614713)
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206 > plot(x, y,type="l",main="Average Concatenated Intron Profile",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.598504,1.005650),xaxt="s",yaxt="s",lwd=2)
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207 > par(mfrow=c(3, 2),mar=c(4, 4, 5, 3.7999999999999998),oma=c(4, 2, 4, 2))
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208 > x<-c(0.000000,50.000000,100.000000)
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209 > y<-c(1.059373,1.056037,1.221481)
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210 > plot(x, y,type="l",main="Average Exon Profile
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211 + (66 <= length < 109 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.619651,1.465777),xaxt="s",yaxt="s",lwd=2)
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212 > x<-c(0.000000,14.285714,28.571429,42.857143,57.142857,71.428571,85.714286,100.000000)
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213 > y<-c(0.692955,0.731861,0.805468,0.827550,0.875920,0.887487,0.909569,0.904311)
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214 > plot(x, y,type="l",main="Average Intron Profile
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215 + (146 <= length < 760 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.619651,1.465777),xaxt="s",yaxt="s",lwd=2)
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216 > x<-c(0.000000,50.000000,100.000000)
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217 > y<-c(0.911765,0.824510,0.840196)
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218 > plot(x, y,type="l",main="Average Exon Profile
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219 + (109 <= length < 165 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.619651,1.465777),xaxt="s",yaxt="s",lwd=2)
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220 > x<-c(0.000000,3.703704,7.407407,11.111111,14.814815,18.518519,22.222222,25.925926,29.629630,33.333333,37.037037,40.740741,44.444444,48.148148,51.851852,55.555556,59.259259,62.962963,66.666667,70.370370,74.074074,77.777778,81.481481,85.185185,88.888889,92.592593,96.296296,100.000000)
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221 > y<-c(0.619651,0.664192,0.754585,0.764629,0.795633,0.800000,0.831004,0.847162,0.857205,0.874236,0.904803,0.894323,0.855022,0.878603,0.885590,0.897380,0.892140,0.921834,0.906550,0.893013,0.884716,0.909607,0.911354,0.927948,0.944978,0.961135,0.951528,0.930131)
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222 > plot(x, y,type="l",main="Average Intron Profile
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223 + (760 <= length < 2301 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.619651,1.465777),xaxt="s",yaxt="s",lwd=2)
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224 > x<-c(0.000000,25.000000,50.000000,75.000000,100.000000)
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225 > y<-c(0.793460,0.823867,0.818703,0.871486,0.955823)
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226 > plot(x, y,type="l",main="Average Exon Profile
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227 + (165 <= length < 529 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.619651,1.465777),xaxt="s",yaxt="s",lwd=2)
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228 > x<-c(0.000000,1.298701,2.597403,3.896104,5.194805,6.493506,7.792208,9.090909,10.389610,11.688312,12.987013,14.285714,15.584416,16.883117,18.181818,19.480519,20.779221,22.077922,23.376623,24.675325,25.974026,27.272727,28.571429,29.870130,31.168831,32.467532,33.766234,35.064935,36.363636,37.662338,38.961039,40.259740,41.558442,42.857143,44.155844,45.454545,46.753247,48.051948,49.350649,50.649351,51.948052,53.246753,54.545455,55.844156,57.142857,58.441558,59.740260,61.038961,62.337662,63.636364,64.935065,66.233766,67.532468,68.831169,70.129870,71.428571,72.727273,74.025974,75.324675,76.623377,77.922078,79.220779,80.519481,81.818182,83.116883,84.415584,85.714286,87.012987,88.311688,89.610390,90.909091,92.207792,93.506494,94.805195,96.103896,97.402597,98.701299,100.000000)
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229 > y<-c(0.651698,0.679080,0.726725,0.748631,0.775465,0.852136,0.873494,0.880066,0.855969,0.870756,0.903067,0.896495,0.888828,0.899781,0.928258,0.937021,0.942497,0.918401,0.907448,0.904710,0.911829,0.903067,0.908543,0.901972,0.915115,0.929901,0.916210,0.928258,0.949617,0.937568,0.921139,0.941402,0.920044,0.934830,0.950712,0.883899,0.911281,0.921139,0.910186,0.914020,0.886637,0.930449,0.915115,0.900329,0.923877,0.905805,0.930449,0.905257,0.938116,0.920591,0.881709,0.897043,0.895947,0.887185,0.881161,0.897043,0.928258,0.904710,0.879518,0.904710,0.906353,0.930997,0.932640,0.910734,0.933735,0.911829,0.927711,0.903614,0.895947,0.926616,0.953450,0.950164,0.945783,0.922782,0.913472,0.928258,0.923877,0.934283)
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230 > plot(x, y,type="l",main="Average Intron Profile
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231 + (2301 <= length < 9365 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.619651,1.465777),xaxt="s",yaxt="s",lwd=2)
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232 > dev.off()
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233 null device
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234 1
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235 >
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236 INFO @ Wed, 17 Sep 2014 07:06:58: #... cong! See ceas_out.pdf for the graphical results of CEAS!
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