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comparison test-data/ceas_out3.log.re_match @ 0:f411ce97a351 draft

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Uploaded initial version 1.0.2-2
author pjbriggs
date Tue, 30 Jun 2015 07:08:05 -0400
parents
children df54f8fcc7a7
comparison
equal deleted inserted replaced
-1:000000000000 0:f411ce97a351
1 ceasBW\ \-\-\ 0\.9\.9\.7\ \(package\ version\ 1\.0\.2\)
2 INFO\ \ \@\ .*\
3 \#\ ARGUMENTS\:\
4 \#\ name\ \=\ ceas
5 \#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
6 \#\ BED\ file\ \=\ .*
7 \#\ WIG\ file\ \=\ .*
8 \#\ extra\ BED\ file\ \=\ None
9 \#\ ChIP\ annotation\ \=\ On
10 \#\ gene\-centered\ annotation\ \=\ \ On
11 \#\ average\ profiling\ \=\ On
12 \#\ dump\ profiles\ \=\ Off
13 \#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
14 \#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
15 \#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
16 \#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
17 \#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp
18 \#\ profiling\ resolution\ \(average\ profiling\)\ \=\ 50\ bp
19 \#\ relative\ distance\ wrt\ TSS\ and\ TTS\ \(average\ profiling\)\ \=\ 3000\ bp\
20 INFO\ \ \@\ .*\ \#1\ read\ the\ gene\ table\.\.\.\
21 INFO\ \ \@\ .*\ \#2\ read\ the\ bed\ file\ of\ ChIP\ regions\.\.\.\
22 INFO\ \ \@\ .*\ \#3\ perform\ gene\-centered\ annotation\.\.\.\
23 INFO\ \ \@\ .*\ \#4\ See\ ceas\.xls\ for\ gene\-centered\ annotation\!\
24 INFO\ \ \@\ .*\ \#5\ read\ the\ pre\-computed\ genome\ bg\ annotation\.\.\.\
25 INFO\ \ \@\ .*\ \#6\ perform\ ChIP\ region\ annotation\.\.\.\
26 INFO\ \ \@\ .*\ \#7\ write\ a\ R\ script\ of\ ChIP\ region\ annotation\.\.\.\
27 INFO\ \ \@\ .*\ \#8\-1\ run\ wig\ profiling\ of\ chr26\.\.\.\
28 INFO\ \ \@\ .*\ \#9\ append\ an\ R\ script\ of\ wig\ profiling\.\.\.\
29
30 R\ version\ 3\.1\.2\ \(2014\-10\-31\)\ \-\-\ \"Pumpkin\ Helmet\"
31 Copyright\ \(C\)\ 2014\ The\ R\ Foundation\ for\ Statistical\ Computing
32 Platform\:\ .*
33
34 R\ is\ free\ software\ and\ comes\ with\ ABSOLUTELY\ NO\ WARRANTY\.
35 You\ are\ welcome\ to\ redistribute\ it\ under\ certain\ conditions\.
36 Type\ \'license\(\)\'\ or\ \'licence\(\)\'\ for\ distribution\ details\.
37
38 \ \ Natural\ language\ support\ but\ running\ in\ an\ English\ locale
39
40 R\ is\ a\ collaborative\ project\ with\ many\ contributors\.
41 Type\ \'contributors\(\)\'\ for\ more\ information\ and
42 \'citation\(\)\'\ on\ how\ to\ cite\ R\ or\ R\ packages\ in\ publications\.
43
44 Type\ \'demo\(\)\'\ for\ some\ demos\,\ \'help\(\)\'\ for\ on\-line\ help\,\ or
45 \'help\.start\(\)\'\ for\ an\ HTML\ browser\ interface\ to\ help\.
46 Type\ \'q\(\)\'\ to\ quit\ R\.
47
48 \>\ \#\ ARGUMENTS\:\
49 \>\ \#\ name\ \=\ ceas
50 \>\ \#\ gene\ annotation\ table\ \=\ .*galGal3\.refGene
51 \>\ \#\ BED\ file\ \=\ .*
52 \>\ \#\ WIG\ file\ \=\ .*
53 \>\ \#\ extra\ BED\ file\ \=\ None
54 \>\ \#\ ChIP\ annotation\ \=\ On
55 \>\ \#\ gene\-centered\ annotation\ \=\ \ On
56 \>\ \#\ average\ profiling\ \=\ On
57 \>\ \#\ dump\ profiles\ \=\ Off
58 \>\ \#\ re\-annotation\ for\ genome\ background\ \(ChIP\ region\ annotation\)\ \=\ False
59 \>\ \#\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
60 \>\ \#\ downstream\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 1000\,2000\,3000\ bp
61 \>\ \#\ bidrectional\ promoter\ sizes\ \(ChIP\ region\ annotation\)\ \=\ 2500\,5000\ bp
62 \>\ \#\ span\ size\ \(gene\-centered\ annotation\)\ \=\ 3000\ bp
63 \>\ \#\ profiling\ resolution\ \(average\ profiling\)\ \=\ 50\ bp
64 \>\ \#\ relative\ distance\ wrt\ TSS\ and\ TTS\ \(average\ profiling\)\ \=\ 3000\ bp
65 \>\ pdf\(\"ceas\.pdf\"\,height\=11\.5\,width\=8\.5\)
66 \>\
67 \>\ \#\ .*
68 \>\ \#\
69 \>\ \#\ ChIP\ annotation
70 \>\ \#\
71 \>\
72 \>\
73 \>\ \#\
74 \>\ \#\ Chromosomal\ Distribution
75 \>\ \#\
76 \>\
77 \>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
78 \>\ r0\<\-c\(100\.0\)
79 \>\ r1\<\-c\(100\.0\)
80 \>\ height\<\-rbind\(r0\,r1\)
81 \>\ names\=c\(\"26\"\)
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\=1\)
83 \>\ text\(x\=c\(100\.0\)\,y\=mp\[1\,\]\,label\=c\(\"100\.0\ \%\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
84 \>\ text\(x\=c\(100\.0\)\,y\=mp\[2\,\]\,label\=c\(\"100\.0\ \%\ \(\<\=4\.9e\-324\)\"\)\,pos\=4\,offset\=0\.2\,cex\=0\.9\)
85 \>\ legend\(\"right\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
86 \>\
87 \>\ \#\
88 \>\ \#\ Promoter\,Bipromoter\,Downstream\,\ Gene\ and\ Regions\ of\ interest
89 \>\ \#\
90 \>\
91 \>\ par\(mfrow\=c\(4\,\ 1\)\,mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
92 \>\ r0\<\-c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)
93 \>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
94 \>\ height\<\-rbind\(r0\,r1\)
95 \>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
96 \>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.757585\)\,cex\.names\=1\)
97 \>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8532425688606797\,\ 3\.616851183410451\,\ 5\.322318854623416\)\,label\=c\(\"1\.9\ \%\"\,\"3\.6\ \%\"\,\"5\.3\ \%\"\)\,pos\=3\,offset\=0\.2\)
98 \>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
99 \+\ \(0\.981\)\"\,\"0\.000\ \%
100 \+\ \(0\.964\)\"\,\"0\.000\ \%
101 \+\ \(0\.947\)\"\)\,pos\=3\,offset\=0\.2\)
102 \>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
103 \>\ r0\<\-c\(0\.03876062889120376\,\ 0\.03876062889120376\)
104 \>\ r1\<\-c\(0\.0\,\ 0\.0\)
105 \>\ height\<\-rbind\(r0\,r1\)
106 \>\ names\=c\(\"\<\=2500\ bp\"\,\"\<\=5000\ bp\"\)
107 \>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Bidirectional\ Promoter\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,0\.071061\)\,cex\.names\=1\)
108 \>\ text\(x\=mp\[1\,\]\,y\=c\(0\.03876062889120376\,\ 0\.03876062889120376\)\,label\=c\(\"0\.04\ \%\"\,\"0\.04\ \%\"\)\,pos\=3\,offset\=0\.2\)
109 \>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
110 \+\ \(1\.000\)\"\,\"0\.000\ \%
111 \+\ \(1\.000\)\"\)\,pos\=3\,offset\=0\.2\)
112 \>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
113 \>\ r0\<\-c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)
114 \>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\)
115 \>\ height\<\-rbind\(r0\,r1\)
116 \>\ names\=c\(\"\<\=1000\ bp\"\,\"\<\=2000\ bp\"\,\"\<\=3000\ bp\"\)
117 \>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Downstream\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,9\.131358\)\,cex\.names\=1\)
118 \>\ text\(x\=mp\[1\,\]\,y\=c\(1\.8290171758036773\,\ 3\.4690762857627364\,\ 4\.980740812519683\)\,label\=c\(\"1\.8\ \%\"\,\"3\.5\ \%\"\,\"5\.0\ \%\"\)\,pos\=3\,offset\=0\.2\)
119 \>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
120 \+\ \(0\.982\)\"\,\"0\.000\ \%
121 \+\ \(0\.965\)\"\,\"0\.000\ \%
122 \+\ \(0\.950\)\"\)\,pos\=3\,offset\=0\.2\)
123 \>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
124 \>\ r0\<\-c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)
125 \>\ r1\<\-c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)
126 \>\ height\<\-rbind\(r0\,r1\)
127 \>\ names\=c\(\"5\'UTR\"\,\"3\'UTR\"\,\"Coding\ Exon\"\,\"Intron\"\,\"All\"\)
128 \>\ mp\<\-barplot\(height\=height\,names\=names\,beside\=TRUE\,horiz\=FALSE\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,main\=\"Gene\"\,ylab\=\"Percentage\ \%\"\,border\=FALSE\,ylim\=c\(0\.000000\,43\.440571\)\,cex\.names\=1\)
129 \>\ text\(x\=mp\[1\,\]\,y\=c\(0\.2034933016788197\,\ 1\.3978051793890356\,\ 2\.359553283752029\,\ 19\.734005184234114\,\ 23\.694856949054\)\,label\=c\(\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.4\ \%\"\,\"19\.7\ \%\"\,\"23\.7\ \%\"\)\,pos\=3\,offset\=0\.2\)
130 \>\ text\(x\=mp\[2\,\]\,y\=c\(0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\,\ 0\.0\)\,label\=c\(\"0\.000\ \%
131 \+\ \(0\.998\)\"\,\"0\.000\ \%
132 \+\ \(0\.986\)\"\,\"0\.000\ \%
133 \+\ \(0\.976\)\"\,\"0\.000\ \%
134 \+\ \(0\.803\)\"\,\"0\.000\ \%
135 \+\ \(0\.763\)\"\)\,pos\=3\,offset\=0\.2\)
136 \>\ legend\(\"topleft\"\,legend\=c\(\"Genome\"\,\"ChIP\ \(p\-value\)\"\)\,col\=c\(\"\#5FA1C1\"\,\"\#EB9D86\"\)\,pch\=15\,bty\=\"n\"\)
137 \>\
138 \>\ \#\
139 \>\ \#\ Distribution\ of\ Genome\ and\ ChIP\ regions\ over\ cis\-regulatory\ element
140 \>\ \#\ Note\ that\ the\ x\ may\ be\ modified\ for\ better\ graphics\ in\ case\ a\ value\ is\ too\ small
141 \>\ \#\ Thus\,\ look\ at\ the\ labels\ of\ the\ pie\ chart\ to\ get\ the\ real\ percentage\ values
142 \>\ \#\
143 \>\
144 \>\ par\(mfcol\=c\(2\,\ 2\)\,mar\=c\(3\,\ 3\,\ 4\,\ 2\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
145 \>\ x\<\-c\(0\.018532\,0\.017055\,0\.016037\,0\.017830\,0\.015092\,0\.014051\,0\.010000\,0\.013833\,0\.023014\,0\.192592\,0\.670292\)
146 \>\ pie\(x\=x\,labels\=c\(\"1\.9\ \%\"\,\"1\.7\ \%\"\,\"1\.6\ \%\"\,\"1\.8\ \%\"\,\"1\.5\ \%\"\,\"1\.4\ \%\"\,\"0\.2\ \%\"\,\"1\.4\ \%\"\,\"2\.3\ \%\"\,\"19\.3\ \%\"\,\"67\.0\ \%\"\)\,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\)
147 \>\ x\<\-c\(0\.000000\,1\.000000\)
148 \>\ y\<\-c\(0\.000000\,1\.000000\)
149 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
150 \>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 1\.9\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 1\.7\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 1\.6\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 1\.8\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 1\.5\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 1\.4\ \%\"\,\"5\'UTR\:\ 0\.2\ \%\"\,\"3\'UTR\:\ 1\.4\ \%\"\,\"Coding\ exon\:\ 2\.3\ \%\"\,\"Intron\:\ 19\.3\ \%\"\,\"Distal\ intergenic\:\ 67\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
151 \>\ x\<\-c\(0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,0\.010000\,1\.000000\)
152 \>\ pie\(x\=x\,labels\=c\(\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"0\.000\ \%\"\,\"100\.0\ \%\"\)\,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\)
153 \>\ x\<\-c\(0\.000000\,1\.000000\)
154 \>\ y\<\-c\(0\.000000\,1\.000000\)
155 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,frame\=FALSE\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
156 \>\ legend\(\"top\"\,legend\=c\(\"Promoter\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Promoter\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(\<\=1000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(1000\-2000\ bp\)\:\ 0\.000\ \%\"\,\"Downstream\ \(2000\-3000\ bp\)\:\ 0\.000\ \%\"\,\"5\'UTR\:\ 0\.000\ \%\"\,\"3\'UTR\:\ 0\.000\ \%\"\,\"Coding\ exon\:\ 0\.000\ \%\"\,\"Intron\:\ 0\.000\ \%\"\,\"Distal\ intergenic\:\ 100\.0\ \%\"\)\,col\=c\(\"\#445FA2\"\,\"\#EB9D86\"\,\"\#799F7A\"\,\"\#6C527F\"\,\"\#5FA1C1\"\,\"\#E8BB77\"\,\"\#A8C5EF\"\,\"\#FDCDB9\"\,\"\#C6E6B5\"\,\"\#F1D5EE\"\,\"\#B4E1F6\"\)\,pch\=15\,bty\=\"n\"\)
157 \>\
158 \>\ \#\
159 \>\ \#\ ChIP\ regions\ over\ the\ genome
160 \>\ \#\
161 \>\
162 \>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
163 \>\ layout\(matrix\(c\(1\,\ 0\,\ 2\,\ 2\)\,\ 2\,\ 2\,\ byrow\ \=\ TRUE\)\,widths\=c\(1\,\ 1\)\,heights\=c\(1\,\ 5\)\)
164 \>\ x\<\-c\(0\.000000\,0\.000000\)
165 \>\ y\<\-c\(0\.000000\,1\.000000\)
166 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"Distribution\ of\ Peak\ Heights\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(0\.000000\,0\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\,cex\=0\.9\)
167 \>\ x\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\)
168 \>\ y\<\-c\(0\.000000\,0\.000000\,1\.000000\,1\.000000\)
169 \>\ polygon\(x\,y\,col\=c\(\"black\"\)\)
170 \>\ x\ \<\-\ c\(0\.000000\)
171 \>\ y\<\-c\(0\.800000\)
172 \>\ lines\(x\,\ y\,xlim\=c\(0\,\ 0\.0\)\,ylim\=c\(0\,\ 1\)\,type\=\"l\"\,col\=c\(\"cyan\"\)\,lwd\=2\)
173 \>\ x\<\-c\(0\.000000\,4127518\.000000\)
174 \>\ y\<\-c\(0\.855556\,1\.144444\)
175 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"ChIP\ Regions\ \(Peaks\)\ over\ Chromosomes\"\,xlab\=\"Chromosome\ Size\ \(bp\)\"\,ylab\=\"Chromosome\"\,xlim\=c\(0\.000000\,4127518\.000000\)\,ylim\=c\(0\.855556\,1\.144444\)\,frame\=FALSE\,xaxt\=\"s\"\,yaxt\=\"n\"\)
176 \>\ start\ \<\-\ c\(4119129\)
177 \>\ end\ \<\-\ c\(4119130\)
178 \>\ vals\ \<\-\ c\(0\.0\)
179 \>\ vals\[vals\ \>\ 0\.0\]\ \<\-\ 0\.0
180 \>\ vals\[vals\ \<\ 0\]\ \<\-\ 0
181 \>\ heights\ \<\-\ 0\.288889\ \*\ \(\(vals\ \-\ 0\)\/\(0\.0\ \-\ 0\)\)\ \+\ 0\.855555555556
182 \>\ for\ \(i\ in\ 1\:length\(heights\)\)\ \{
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\(\"\#CC0000\"\)\)
184 \+\ \}
185 \>\ mtext\(\"26\"\,side\=2\,line\=0\,outer\=FALSE\,at\=1\.0\)
186 \>\ par\(mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
187 \>\ layout\(matrix\(c\(1\,\ 2\,\ 3\,\ 3\,\ 4\,\ 5\)\,\ 3\,\ 2\,\ byrow\ \=\ TRUE\)\,widths\=c\(1\,\ 1\)\,heights\=c\(1\,\ 1\,\ 1\)\)
188 \>\ x\<\-c\(\-3000\.000000\,\-2950\.000000\,\-2900\.000000\,\-2850\.000000\,\-2800\.000000\,\-2750\.000000\,\-2700\.000000\,\-2650\.000000\,\-2600\.000000\,\-2550\.000000\,\-2500\.000000\,\-2450\.000000\,\-2400\.000000\,\-2350\.000000\,\-2300\.000000\,\-2250\.000000\,\-2200\.000000\,\-2150\.000000\,\-2100\.000000\,\-2050\.000000\,\-2000\.000000\,\-1950\.000000\,\-1900\.000000\,\-1850\.000000\,\-1800\.000000\,\-1750\.000000\,\-1700\.000000\,\-1650\.000000\,\-1600\.000000\,\-1550\.000000\,\-1500\.000000\,\-1450\.000000\,\-1400\.000000\,\-1350\.000000\,\-1300\.000000\,\-1250\.000000\,\-1200\.000000\,\-1150\.000000\,\-1100\.000000\,\-1050\.000000\,\-1000\.000000\,\-950\.000000\,\-900\.000000\,\-850\.000000\,\-800\.000000\,\-750\.000000\,\-700\.000000\,\-650\.000000\,\-600\.000000\,\-550\.000000\,\-500\.000000\,\-450\.000000\,\-400\.000000\,\-350\.000000\,\-300\.000000\,\-250\.000000\,\-200\.000000\,\-150\.000000\,\-100\.000000\,\-50\.000000\,0\.000000\,50\.000000\,100\.000000\,150\.000000\,200\.000000\,250\.000000\,300\.000000\,350\.000000\,400\.000000\,450\.000000\,500\.000000\,550\.000000\,600\.000000\,650\.000000\,700\.000000\,750\.000000\,800\.000000\,850\.000000\,900\.000000\,950\.000000\,1000\.000000\,1050\.000000\,1100\.000000\,1150\.000000\,1200\.000000\,1250\.000000\,1300\.000000\,1350\.000000\,1400\.000000\,1450\.000000\,1500\.000000\,1550\.000000\,1600\.000000\,1650\.000000\,1700\.000000\,1750\.000000\,1800\.000000\,1850\.000000\,1900\.000000\,1950\.000000\,2000\.000000\,2050\.000000\,2100\.000000\,2150\.000000\,2200\.000000\,2250\.000000\,2300\.000000\,2350\.000000\,2400\.000000\,2450\.000000\,2500\.000000\,2550\.000000\,2600\.000000\,2650\.000000\,2700\.000000\,2750\.000000\,2800\.000000\,2850\.000000\,2900\.000000\,2950\.000000\,3000\.000000\)
189 \>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
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\)
191 \>\ abline\(v\=0\.000000\,lty\=2\,col\=c\(\"black\"\)\)
192 \>\ x\<\-c\(\-3000\.000000\,\-2950\.000000\,\-2900\.000000\,\-2850\.000000\,\-2800\.000000\,\-2750\.000000\,\-2700\.000000\,\-2650\.000000\,\-2600\.000000\,\-2550\.000000\,\-2500\.000000\,\-2450\.000000\,\-2400\.000000\,\-2350\.000000\,\-2300\.000000\,\-2250\.000000\,\-2200\.000000\,\-2150\.000000\,\-2100\.000000\,\-2050\.000000\,\-2000\.000000\,\-1950\.000000\,\-1900\.000000\,\-1850\.000000\,\-1800\.000000\,\-1750\.000000\,\-1700\.000000\,\-1650\.000000\,\-1600\.000000\,\-1550\.000000\,\-1500\.000000\,\-1450\.000000\,\-1400\.000000\,\-1350\.000000\,\-1300\.000000\,\-1250\.000000\,\-1200\.000000\,\-1150\.000000\,\-1100\.000000\,\-1050\.000000\,\-1000\.000000\,\-950\.000000\,\-900\.000000\,\-850\.000000\,\-800\.000000\,\-750\.000000\,\-700\.000000\,\-650\.000000\,\-600\.000000\,\-550\.000000\,\-500\.000000\,\-450\.000000\,\-400\.000000\,\-350\.000000\,\-300\.000000\,\-250\.000000\,\-200\.000000\,\-150\.000000\,\-100\.000000\,\-50\.000000\,0\.000000\,50\.000000\,100\.000000\,150\.000000\,200\.000000\,250\.000000\,300\.000000\,350\.000000\,400\.000000\,450\.000000\,500\.000000\,550\.000000\,600\.000000\,650\.000000\,700\.000000\,750\.000000\,800\.000000\,850\.000000\,900\.000000\,950\.000000\,1000\.000000\,1050\.000000\,1100\.000000\,1150\.000000\,1200\.000000\,1250\.000000\,1300\.000000\,1350\.000000\,1400\.000000\,1450\.000000\,1500\.000000\,1550\.000000\,1600\.000000\,1650\.000000\,1700\.000000\,1750\.000000\,1800\.000000\,1850\.000000\,1900\.000000\,1950\.000000\,2000\.000000\,2050\.000000\,2100\.000000\,2150\.000000\,2200\.000000\,2250\.000000\,2300\.000000\,2350\.000000\,2400\.000000\,2450\.000000\,2500\.000000\,2550\.000000\,2600\.000000\,2650\.000000\,2700\.000000\,2750\.000000\,2800\.000000\,2850\.000000\,2900\.000000\,2950\.000000\,3000\.000000\)
193 \>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\)
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\)
195 \>\ abline\(v\=0\.000000\,lty\=2\,col\=c\(\"black\"\)\)
196 \>\ x\<\-c\(\-1000\.000000\,\-950\.000000\,\-900\.000000\,\-850\.000000\,\-800\.000000\,\-750\.000000\,\-700\.000000\,\-650\.000000\,\-600\.000000\,\-550\.000000\,\-500\.000000\,\-450\.000000\,\-400\.000000\,\-350\.000000\,\-300\.000000\,\-250\.000000\,\-200\.000000\,\-150\.000000\,\-100\.000000\,\-50\.000000\,0\.000000\,50\.000000\,100\.000000\,150\.000000\,200\.000000\,250\.000000\,300\.000000\,350\.000000\,400\.000000\,450\.000000\,500\.000000\,550\.000000\,600\.000000\,650\.000000\,700\.000000\,750\.000000\,800\.000000\,850\.000000\,900\.000000\,950\.000000\,1000\.000000\,1050\.000000\,1100\.000000\,1150\.000000\,1200\.000000\,1250\.000000\,1300\.000000\,1350\.000000\,1400\.000000\,1450\.000000\,1500\.000000\,1550\.000000\,1600\.000000\,1650\.000000\,1700\.000000\,1750\.000000\,1800\.000000\,1850\.000000\,1900\.000000\,1950\.000000\,2000\.000000\,2050\.000000\,2100\.000000\,2150\.000000\,2200\.000000\,2250\.000000\,2300\.000000\,2350\.000000\,2400\.000000\,2450\.000000\,2500\.000000\,2550\.000000\,2600\.000000\,2650\.000000\,2700\.000000\,2750\.000000\,2800\.000000\,2850\.000000\,2900\.000000\,2950\.000000\,3000\.000000\,3050\.000000\,3100\.000000\,3150\.000000\,3200\.000000\,3250\.000000\,3300\.000000\,3350\.000000\,3400\.000000\,3450\.000000\,3500\.000000\,3550\.000000\,3600\.000000\,3650\.000000\,3700\.000000\,3750\.000000\,3800\.000000\,3850\.000000\,3900\.000000\,3950\.000000\,4000\.000000\)
197 \>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
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\)
199 \>\ abline\(v\=0\.000000\,lty\=2\,col\=c\(\"black\"\)\)
200 \>\ abline\(v\=3000\.000000\,lty\=2\,col\=c\(\"black\"\)\)
201 \>\ x\<\-c\(0\.000000\,3\.333333\,6\.666667\,10\.000000\,13\.333333\,16\.666667\,20\.000000\,23\.333333\,26\.666667\,30\.000000\,33\.333333\,36\.666667\,40\.000000\,43\.333333\,46\.666667\,50\.000000\,53\.333333\,56\.666667\,60\.000000\,63\.333333\,66\.666667\,70\.000000\,73\.333333\,76\.666667\,80\.000000\,83\.333333\,86\.666667\,90\.000000\,93\.333333\,96\.666667\,100\.000000\)
202 \>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
203 \>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Concatenated\ Exon\ Profile\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,20000\.000000\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
204 \>\ x\<\-c\(0\.000000\,3\.333333\,6\.666667\,10\.000000\,13\.333333\,16\.666667\,20\.000000\,23\.333333\,26\.666667\,30\.000000\,33\.333333\,36\.666667\,40\.000000\,43\.333333\,46\.666667\,50\.000000\,53\.333333\,56\.666667\,60\.000000\,63\.333333\,66\.666667\,70\.000000\,73\.333333\,76\.666667\,80\.000000\,83\.333333\,86\.666667\,90\.000000\,93\.333333\,96\.666667\,100\.000000\)
205 \>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\)
206 \>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Concatenated\ Intron\ Profile\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,20000\.000000\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
207 \>\ par\(mfrow\=c\(3\,\ 2\)\,mar\=c\(4\,\ 4\,\ 5\,\ 3\.8\)\,oma\=c\(4\,\ 2\,\ 4\,\ 2\)\)
208 \>\ x\<\-c\(\-3\.000000\,3\.000000\)
209 \>\ y\<\-c\(0\.000000\,1\.000000\)
210 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
211 \>\ x\<\-c\(\-3\.000000\,3\.000000\)
212 \>\ y\<\-c\(0\.000000\,1\.000000\)
213 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
214 \>\ x\<\-c\(\-3\.000000\,3\.000000\)
215 \>\ y\<\-c\(0\.000000\,1\.000000\)
216 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
217 \>\ x\<\-c\(\-3\.000000\,3\.000000\)
218 \>\ y\<\-c\(0\.000000\,1\.000000\)
219 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
220 \>\ x\<\-c\(\-3\.000000\,3\.000000\)
221 \>\ y\<\-c\(0\.000000\,1\.000000\)
222 \>\ plot\(x\,\ y\,type\=\"n\"\,main\=\"\"\,xlab\=\"\"\,ylab\=\"\"\,xlim\=c\(\-3\.000000\,3\.000000\)\,ylim\=c\(0\.000000\,1\.000000\)\,axes\=FALSE\,xaxt\=\"s\"\,yaxt\=\"s\"\)
223 \>\ x\<\-c\(0\.000000\,4\.761905\,9\.523810\,14\.285714\,19\.047619\,23\.809524\,28\.571429\,33\.333333\,38\.095238\,42\.857143\,47\.619048\,52\.380952\,57\.142857\,61\.904762\,66\.666667\,71\.428571\,76\.190476\,80\.952381\,85\.714286\,90\.476190\,95\.238095\,100\.000000\)
224 \>\ y\<\-c\(0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,0\.000000\,20000\.000000\,0\.000000\)
225 \>\ plot\(x\,\ y\,type\=\"l\"\,main\=\"Average\ Intron\ Profile
226 \+\ \(685\ \<\=\ length\ \<\ 2653\ bp\)\"\,xlab\=\"Relative\ Location\ \(\%\)\"\,ylab\=\"Average\ Profile\"\,col\=c\(\"\#C8524D\"\)\,ylim\=c\(0\.000000\,24000\.000000\)\,xaxt\=\"s\"\,yaxt\=\"s\"\,lwd\=2\)
227 \>\ dev\.off\(\)
228 null\ device\
229 \ \ \ \ \ \ \ \ \ \ 1\
230 \>\
231 INFO\ \ \@\ .*\ \#\.\.\.\ cong\!\ See\ ceas\.pdf\ for\ the\ graphical\ results\ of\ CEAS\!\