[Patchwork-commits] r149 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/R pkg/patchworkCG/R www
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 28 15:02:29 CEST 2012
Author: sebastian_d
Date: 2012-09-28 15:02:29 +0200 (Fri, 28 Sep 2012)
New Revision: 149
Modified:
.git/COMMIT_EDITMSG
.git/index
.git/logs/HEAD
.git/logs/refs/heads/master
.git/logs/refs/remotes/origin/master
.git/refs/heads/master
.git/refs/remotes/origin/master
pkg/patchwork/R/patchwork.smoothing.r
pkg/patchworkCG/R/patchwork.CG.plot.r
www/cg_requ.php
Log:
update to reflect that bz2 mastervar files work with patchworkCG as input
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2012-09-11 13:32:36 UTC (rev 148)
+++ .git/COMMIT_EDITMSG 2012-09-28 13:02:29 UTC (rev 149)
@@ -1 +1 @@
-Updated homepage info
+updated to reflect that bz2 mastervar files will also work to homepage
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2012-09-11 13:32:36 UTC (rev 148)
+++ .git/logs/HEAD 2012-09-28 13:02:29 UTC (rev 149)
@@ -17,3 +17,4 @@
dce9edf1dd01665c7e266395f3ad217738315c02 d5df007a35dcbf109f45dd0c15d100996ee41b9b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1346420997 +0200 commit: update homepage info slightly
d5df007a35dcbf109f45dd0c15d100996ee41b9b 0ea92759a953e9e176617cf22b4050ce2fed0bef Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1346421578 +0200 commit: updated changelog and description
0ea92759a953e9e176617cf22b4050ce2fed0bef 0de5cb34cc64ebefb98b257d93c88bfd65c7f640 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1347370308 +0200 commit: Updated homepage info
+0de5cb34cc64ebefb98b257d93c88bfd65c7f640 53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1348837295 +0200 commit: updated to reflect that bz2 mastervar files will also work to homepage
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2012-09-11 13:32:36 UTC (rev 148)
+++ .git/logs/refs/heads/master 2012-09-28 13:02:29 UTC (rev 149)
@@ -17,3 +17,4 @@
dce9edf1dd01665c7e266395f3ad217738315c02 d5df007a35dcbf109f45dd0c15d100996ee41b9b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1346420997 +0200 commit: update homepage info slightly
d5df007a35dcbf109f45dd0c15d100996ee41b9b 0ea92759a953e9e176617cf22b4050ce2fed0bef Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1346421578 +0200 commit: updated changelog and description
0ea92759a953e9e176617cf22b4050ce2fed0bef 0de5cb34cc64ebefb98b257d93c88bfd65c7f640 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1347370308 +0200 commit: Updated homepage info
+0de5cb34cc64ebefb98b257d93c88bfd65c7f640 53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1348837295 +0200 commit: updated to reflect that bz2 mastervar files will also work to homepage
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2012-09-11 13:32:36 UTC (rev 148)
+++ .git/logs/refs/remotes/origin/master 2012-09-28 13:02:29 UTC (rev 149)
@@ -17,3 +17,4 @@
dce9edf1dd01665c7e266395f3ad217738315c02 d5df007a35dcbf109f45dd0c15d100996ee41b9b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1346421012 +0200 update by push
d5df007a35dcbf109f45dd0c15d100996ee41b9b 0ea92759a953e9e176617cf22b4050ce2fed0bef Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1346421591 +0200 update by push
0ea92759a953e9e176617cf22b4050ce2fed0bef 0de5cb34cc64ebefb98b257d93c88bfd65c7f640 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1347370323 +0200 update by push
+0de5cb34cc64ebefb98b257d93c88bfd65c7f640 53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1348837313 +0200 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2012-09-11 13:32:36 UTC (rev 148)
+++ .git/refs/heads/master 2012-09-28 13:02:29 UTC (rev 149)
@@ -1 +1 @@
-0de5cb34cc64ebefb98b257d93c88bfd65c7f640
+53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2012-09-11 13:32:36 UTC (rev 148)
+++ .git/refs/remotes/origin/master 2012-09-28 13:02:29 UTC (rev 149)
@@ -1 +1 @@
-0de5cb34cc64ebefb98b257d93c88bfd65c7f640
+53fb1e3cd198d3f12e30ab52891a42e19f5bfdfc
Modified: pkg/patchwork/R/patchwork.smoothing.r
===================================================================
--- pkg/patchwork/R/patchwork.smoothing.r 2012-09-11 13:32:36 UTC (rev 148)
+++ pkg/patchwork/R/patchwork.smoothing.r 2012-09-28 13:02:29 UTC (rev 149)
@@ -26,6 +26,7 @@
#attach(data[as.character(data$chr)==c & data$pos<ideogram$start[i],])
+ #index of we are on the right chromosome and before centromere
ix = as.character(data$chr)==c & data$pos<ideogram$start[i]
norm = data$norm[ix]
pos = data$pos[ix]
@@ -44,6 +45,7 @@
for (i in 1:nsegs)
{
j=kbposix[i]
+ #Create 50 bp windows to take median coverage of for tumor and normal/reference
ix <- (j-(window/2)):(j+(window/2))
coverage[i] <- mean(norm[ix], na.rm=T)
refcoverage[i] <- mean(reference[ix], na.rm=T)
@@ -57,6 +59,7 @@
i=which(as.character(ideogram$chr)==c) #!!
#attach(data[as.character(data$chr)==c & data$pos>ideogram$end[i],])
+ #index of we are on the right chromosome and after centromere
ix = as.character(data$chr)==c & data$pos>ideogram$end[i]
norm = data$norm[ix]
pos = data$pos[ix]
@@ -72,6 +75,7 @@
for (i in 1:nsegs)
{
j=kbposix[i]
+ #Create 50 bp windows to take median coverage of for tumor and normal/reference
ix <- (j-(window/2)):(j+(window/2))
coverage[i] <- median(norm[ix], na.rm=T)
refcoverage[i] <- median(reference[ix], na.rm=T)
@@ -81,6 +85,8 @@
#detach()
}
colnames(kbsegs) <- c('chr','pos','coverage','refcoverage')
+
+ #the normalized coverage ratio is the tumors coverage over the reference coverage which should normalize for positional effect.
kbsegs$ratio <- kbsegs$coverage/kbsegs$refcoverage
return(kbsegs)
}
Modified: pkg/patchworkCG/R/patchwork.CG.plot.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.plot.r 2012-09-11 13:32:36 UTC (rev 148)
+++ pkg/patchworkCG/R/patchwork.CG.plot.r 2012-09-28 13:02:29 UTC (rev 149)
@@ -9,7 +9,7 @@
if(manual_file_input==TRUE)
{
#Prompt for input of path to your files.
- cat("ex: ~/user/documents/projekt/masterVarBeta-123-456-ASM-T1-N1.tsv")
+ cat("ex: ~/user/documents/projekt/masterVarBeta-123-456-ASM-T1-N1.tsv.bz2")
cat("\n","Enter complete path AND filename to your masterVarBeta file:","\n")
mv = scan(n=1,what=character())
cat("\n","ex: ~/user/documents/projekt/somaticCnvSegmentsNondiploidBeta-123-456-ASM-T1-N1.tsv")
Modified: www/cg_requ.php
===================================================================
--- www/cg_requ.php 2012-09-11 13:32:36 UTC (rev 148)
+++ www/cg_requ.php 2012-09-28 13:02:29 UTC (rev 149)
@@ -1,11 +1,12 @@
-To succesfully run patchworkCG you will need an unpacked
+To succesfully run patchworkCG you will need an
<a href="http://media.completegenomics.com/documents/DataFileFormats+Cancer+Pipeline+2.0.pdf"
target="_blank" style="text-decoration:none;">
CompleteGenomics tumor genome data ASM directory</a>.<br />
Specifically the files ASM/masterVarBeta, CNV/depthOfCoverage and CNV/somaticCnvSegmentsNondiploidBeta are used. <br /><br />
+<!--
Here are some helpful commands for unpacking your CompleteGenomics data (UNIX).<br /><br />
To unpack .tar files:<br />
<pre>
@@ -15,4 +16,6 @@
To unpack .bz2 files: <br />
<pre>
bunzip2 filename.bz2
-</pre>
\ No newline at end of file
+</pre>
+
+-->
\ No newline at end of file
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