Mercurial > repos > pjbriggs > ceas

diff test-data/ceas_out2.log @ 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
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ceas_out2.log	Tue Jun 30 07:08:05 2015 -0400
@@ -0,0 +1,236 @@
+ceas -- 0.9.9.7 (package version 1.0.2)
+INFO  @ Tue, 23 Jun 2015 11:24:09: 
+# ARGUMENTS: 
+# name = ceas
+# gene annotation table = galGal3.refGene
+# BED file = ceas_in.bed
+# WIG file = ceas_in_stp1000.wig
+# extra BED file = None
+# ChIP annotation = On
+# gene-centered annotation =  On
+# average profiling = On
+# dump profiles = Off
+# re-annotation for genome background (ChIP region annotation) = False
+# promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
+# downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
+# bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
+# span size (gene-centered annotation) = 3000 bp
+# profiling resolution (average profiling) = 50 bp
+# relative distance wrt TSS and TTS (average profiling) = 3000 bp 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #1 read the gene table... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #2 read the bed file of ChIP regions... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #3 perform gene-centered annotation... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #4 See ceas.xls for gene-centered annotation! 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #5 read the pre-computed genome bg annotation... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #6 perform ChIP region annotation... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #7 write a R script of ChIP region annotation... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #8-1 run wig profiling of chr26... 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #9 append an R script of wig profiling... 
+
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-redhat-linux-gnu (64-bit)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type 'license()' or 'licence()' for distribution details.
+
+  Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> # ARGUMENTS: 
+> # name = ceas
+> # gene annotation table = galGal3.refGene
+> # BED file = ceas_in.bed
+> # WIG file = ceas_in_stp1000.wig
+> # extra BED file = None
+> # ChIP annotation = On
+> # gene-centered annotation =  On
+> # average profiling = On
+> # dump profiles = Off
+> # re-annotation for genome background (ChIP region annotation) = False
+> # promoter sizes (ChIP region annotation) = 1000,2000,3000 bp
+> # downstream sizes (ChIP region annotation) = 1000,2000,3000 bp
+> # bidrectional promoter sizes (ChIP region annotation) = 2500,5000 bp
+> # span size (gene-centered annotation) = 3000 bp
+> # profiling resolution (average profiling) = 50 bp
+> # relative distance wrt TSS and TTS (average profiling) = 3000 bp
+> pdf("ceas.pdf",height=11.5,width=8.5)
+> 
+> # 11:24:09 Tue, 23 Jun 2015
+> # 
+> # ChIP annotation
+> # 
+> 
+> 
+> # 
+> # Chromosomal Distribution
+> # 
+> 
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> r0<-c(100.0)
+> r1<-c(100.0)
+> height<-rbind(r0,r1)
+> names=c("26")
+> 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)
+> text(x=c(100.0),y=mp[1,],label=c("100.0 %"),pos=4,offset=0.2,cex=0.9)
+> text(x=c(100.0),y=mp[2,],label=c("100.0 % (<=4.9e-324)"),pos=4,offset=0.2,cex=0.9)
+> legend("right",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> 
+> # 
+> # Promoter,Bipromoter,Downstream, Gene and Regions of interest
+> # 
+> 
+> par(mfrow=c(4, 1),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> r0<-c(1.8532425688606797, 3.616851183410451, 5.322318854623416)
+> r1<-c(0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=1000 bp","<=2000 bp","<=3000 bp")
+> 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)
+> 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)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0),label=c("0.000 %
++ (0.981)","0.000 %
++ (0.964)","0.000 %
++ (0.947)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(0.03876062889120376, 0.03876062889120376)
+> r1<-c(0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=2500 bp","<=5000 bp")
+> 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)
+> text(x=mp[1,],y=c(0.03876062889120376, 0.03876062889120376),label=c("0.04 %","0.04 %"),pos=3,offset=0.2)
+> text(x=mp[2,],y=c(0.0, 0.0),label=c("0.000 %
++ (1.000)","0.000 %
++ (1.000)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(1.8290171758036773, 3.4690762857627364, 4.980740812519683)
+> r1<-c(0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("<=1000 bp","<=2000 bp","<=3000 bp")
+> 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)
+> 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)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0),label=c("0.000 %
++ (0.982)","0.000 %
++ (0.965)","0.000 %
++ (0.950)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> r0<-c(0.2034933016788197, 1.3978051793890356, 2.359553283752029, 19.734005184234114, 23.694856949054)
+> r1<-c(0.0, 0.0, 0.0, 0.0, 0.0)
+> height<-rbind(r0,r1)
+> names=c("5'UTR","3'UTR","Coding Exon","Intron","All")
+> 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)
+> 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)
+> text(x=mp[2,],y=c(0.0, 0.0, 0.0, 0.0, 0.0),label=c("0.000 %
++ (0.998)","0.000 %
++ (0.986)","0.000 %
++ (0.976)","0.000 %
++ (0.803)","0.000 %
++ (0.763)"),pos=3,offset=0.2)
+> legend("topleft",legend=c("Genome","ChIP (p-value)"),col=c("#5FA1C1","#EB9D86"),pch=15,bty="n")
+> 
+> # 
+> # Distribution of Genome and ChIP regions over cis-regulatory element
+> # Note that the x may be modified for better graphics in case a value is too small
+> # Thus, look at the labels of the pie chart to get the real percentage values
+> # 
+> 
+> par(mfcol=c(2, 2),mar=c(3, 3, 4, 2.8),oma=c(4, 2, 4, 2))
+> x<-c(0.018532,0.017055,0.016037,0.017830,0.015092,0.014051,0.010000,0.013833,0.023014,0.192592,0.670292)
+> 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)
+> x<-c(0.000000,1.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
+> 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")
+> x<-c(0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,0.010000,1.000000)
+> 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)
+> x<-c(0.000000,1.000000)
+> y<-c(0.000000,1.000000)
+> plot(x, y,type="n",main="",xlab="",ylab="",frame=FALSE,axes=FALSE,xaxt="s",yaxt="s")
+> 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")
+> 
+> # 
+> # ChIP regions over the genome
+> # 
+> 
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> layout(matrix(c(1, 0, 2, 2), 2, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 5))
+> x<-c(0.000000,0.000000)
+> y<-c(0.000000,1.000000)
+> 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)
+> x<-c(0.000000,0.000000,0.000000,0.000000)
+> y<-c(0.000000,0.000000,1.000000,1.000000)
+> polygon(x,y,col=c("black"))
+> x <- c(0.000000)
+> y<-c(0.800000)
+> lines(x, y,xlim=c(0, 0.0),ylim=c(0, 1),type="l",col=c("cyan"),lwd=2)
+> x<-c(0.000000,4127518.000000)
+> y<-c(0.855556,1.144444)
+> 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")
+> start <- c(4119129)
+> end <- c(4119130)
+> vals <- c(0.0)
+> vals[vals > 0.0] <- 0.0
+> vals[vals < 0] <- 0
+> heights <- 0.288889 * ((vals - 0)/(0.0 - 0)) + 0.855555555556
+> for (i in 1:length(heights)) {
++ 	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"))
++ }
+> mtext("26",side=2,line=0,outer=FALSE,at=1.0)
+> par(mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> layout(matrix(c(1, 2, 3, 3, 4, 5), 3, 2, byrow = TRUE),widths=c(1, 1),heights=c(1, 1, 1))
+> 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)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> 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)
+> abline(v=0.000000,lty=2,col=c("black"))
+> 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)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000)
+> 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)
+> abline(v=0.000000,lty=2,col=c("black"))
+> 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)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,238.095238,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,217.391304,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> 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)
+> abline(v=0.000000,lty=2,col=c("black"))
+> abline(v=3000.000000,lty=2,col=c("black"))
+> 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)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,250.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Concatenated Exon Profile",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,250.000000),xaxt="s",yaxt="s",lwd=2)
+> 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)
+> 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)
+> plot(x, y,type="l",main="Average Concatenated Intron Profile",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,250.000000),xaxt="s",yaxt="s",lwd=2)
+> par(mfrow=c(3, 2),mar=c(4, 4, 5, 3.8),oma=c(4, 2, 4, 2))
+> x<-c(0.000000,50.000000,100.000000)
+> y<-c(0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Exon Profile
++ (56 <= length < 109 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,25.000000,50.000000,75.000000,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Intron Profile
++ (110 <= length < 345 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,50.000000,100.000000)
+> y<-c(0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Exon Profile
++ (109 <= length < 160 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,11.111111,22.222222,33.333333,44.444444,55.555556,66.666667,77.777778,88.888889,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Intron Profile
++ (344 <= length < 686 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> x<-c(0.000000,33.333333,66.666667,100.000000)
+> y<-c(0.000000,0.000000,0.000000,0.000000)
+> plot(x, y,type="l",main="Average Exon Profile
++ (160 <= length < 375 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> 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)
+> y<-c(0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,0.000000,110.497238,0.000000)
+> plot(x, y,type="l",main="Average Intron Profile
++ (685 <= length < 2653 bp)",xlab="Relative Location (%)",ylab="Average Profile",col=c("#C8524D"),ylim=c(0.000000,132.596685),xaxt="s",yaxt="s",lwd=2)
+> dev.off()
+null device 
+          1 
+> 
+INFO  @ Tue, 23 Jun 2015 11:24:09: #... cong! See ceas.pdf for the graphical results of CEAS!