[Patchwork-commits] r154 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/patchwork/R pkg/patchwork/man pkg/patchworkCG/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 4 11:24:06 CET 2013
Author: sebastian_d
Date: 2013-01-04 11:24:05 +0100 (Fri, 04 Jan 2013)
New Revision: 154
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.plot.r
pkg/patchwork/man/patchwork.plot.Rd
pkg/patchworkCG/R/patchwork.CG.copynumbers.r
pkg/patchworkCG/R/zzz.R
Log:
update to patchwork.alleledata function in patchwork. Also updated documentation for mpileup usage
Modified: .git/COMMIT_EDITMSG
===================================================================
--- .git/COMMIT_EDITMSG 2012-11-30 10:54:10 UTC (rev 153)
+++ .git/COMMIT_EDITMSG 2013-01-04 10:24:05 UTC (rev 154)
@@ -1 +1 @@
-more fixes regarding assignAI
+update to patchwork.alleledata function in patchwork. Also updated documentation for mpileup usage
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2012-11-30 10:54:10 UTC (rev 153)
+++ .git/logs/HEAD 2013-01-04 10:24:05 UTC (rev 154)
@@ -22,3 +22,4 @@
121e1229bbfdb5e93aea7268469f568c16388ada ac036caf16d37514a79e980f6da0e562c404bf57 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1352983874 +0100 commit: small homepage changes
ac036caf16d37514a79e980f6da0e562c404bf57 eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354267289 +0100 commit: Commented out assignAI which shouldent have been in use from patchwork
eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a c7cdeb76a91652d654a622c343d9d40a38d673bb Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354272864 +0100 commit: more fixes regarding assignAI
+c7cdeb76a91652d654a622c343d9d40a38d673bb 684bd069c85e2e51e3e570ea00e9b586993e694b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1357295102 +0100 commit: update to patchwork.alleledata function in patchwork. Also updated documentation for mpileup usage
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2012-11-30 10:54:10 UTC (rev 153)
+++ .git/logs/refs/heads/master 2013-01-04 10:24:05 UTC (rev 154)
@@ -22,3 +22,4 @@
121e1229bbfdb5e93aea7268469f568c16388ada ac036caf16d37514a79e980f6da0e562c404bf57 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1352983874 +0100 commit: small homepage changes
ac036caf16d37514a79e980f6da0e562c404bf57 eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354267289 +0100 commit: Commented out assignAI which shouldent have been in use from patchwork
eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a c7cdeb76a91652d654a622c343d9d40a38d673bb Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354272864 +0100 commit: more fixes regarding assignAI
+c7cdeb76a91652d654a622c343d9d40a38d673bb 684bd069c85e2e51e3e570ea00e9b586993e694b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1357295102 +0100 commit: update to patchwork.alleledata function in patchwork. Also updated documentation for mpileup usage
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2012-11-30 10:54:10 UTC (rev 153)
+++ .git/logs/refs/remotes/origin/master 2013-01-04 10:24:05 UTC (rev 154)
@@ -22,3 +22,4 @@
121e1229bbfdb5e93aea7268469f568c16388ada ac036caf16d37514a79e980f6da0e562c404bf57 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1352983892 +0100 update by push
ac036caf16d37514a79e980f6da0e562c404bf57 eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354267311 +0100 update by push
eb98d72bfc02cfe4a0b30f1a2a0a64107444e40a c7cdeb76a91652d654a622c343d9d40a38d673bb Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1354272883 +0100 update by push
+c7cdeb76a91652d654a622c343d9d40a38d673bb 684bd069c85e2e51e3e570ea00e9b586993e694b Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1357295117 +0100 update by push
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2012-11-30 10:54:10 UTC (rev 153)
+++ .git/refs/heads/master 2013-01-04 10:24:05 UTC (rev 154)
@@ -1 +1 @@
-c7cdeb76a91652d654a622c343d9d40a38d673bb
+684bd069c85e2e51e3e570ea00e9b586993e694b
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2012-11-30 10:54:10 UTC (rev 153)
+++ .git/refs/remotes/origin/master 2013-01-04 10:24:05 UTC (rev 154)
@@ -1 +1 @@
-c7cdeb76a91652d654a622c343d9d40a38d673bb
+684bd069c85e2e51e3e570ea00e9b586993e694b
Modified: pkg/patchwork/R/patchwork.plot.r
===================================================================
--- pkg/patchwork/R/patchwork.plot.r 2012-11-30 10:54:10 UTC (rev 153)
+++ pkg/patchwork/R/patchwork.plot.r 2013-01-04 10:24:05 UTC (rev 154)
@@ -27,8 +27,33 @@
if(is.null(alf))
{
cat("Initiating Allele Data Generation \n")
- if (!is.null(Normal.pileup)) normalalf <- patchwork.alleledata(Normal.pileup, vcf=Normal.vcf)
- alf = patchwork.alleledata(Tumor.pileup, normalalf=normalalf,Tumor.vcf)
+
+ #If Normal.pileup exists, use with normal.vcf (if mpileup) or without (if pileup) to
+ #create normalalf in patchwork.alleledata()
+
+ #Note that right not normalalf isnt even enabled.
+ #if (!is.null(Normal.pileup)) normalalf <- patchwork.alleledata(Normal.pileup, vcf=Normal.vcf)
+
+ alf = patchwork.alleledata(Tumor.pileup,
+ #normalalf=normalalf,
+ vcf=Tumor.vcf)
+
+ # if(!is.null(Normal.pileup) & !is.null(Reference))
+ # {
+ # cat("ATTENTION: You have values for both Reference and Normal.pileup parameters. Normal will \n
+ # be used for allele extraction from pileup.")
+ # }
+
+ # #If both normal.pileup and normal.vcf exists use them to create a normal alf (samtools mpileup)
+ # if (!is.null(Normal.pileup) & !is.null(Normal.vcf)) normalalf <- patchwork.alleledata(Normal.pileup, vcf=Normal.vcf)
+ # alf = patchwork.alleledata(Tumor.pileup, normalalf=normalalf,Tumor.vcf)
+
+ # #If we have normal.pileup but not normal.vcf (samtools pileup)
+ # if (!is.null(Normal.pileup) & is.null(Normal.vcf)) normalalf <- patchwork.alleledata(Normal.pileup)
+ # alf = patchwork.alleledata(Tumor.pileup, normalalf=normalalf)
+
+ # #No normal sample
+ # if (!is.null(Reference) & is.null(Normal.pileup)) alf <- patchwork.alleledata(Tumor.pileup)
cat("Allele Data Generation Complete \n")
save(alf, normalalf,file=paste(name,"_pile.alleles.Rdata",sep=""))
}
Modified: pkg/patchwork/man/patchwork.plot.Rd
===================================================================
--- pkg/patchwork/man/patchwork.plot.Rd 2012-11-30 10:54:10 UTC (rev 153)
+++ pkg/patchwork/man/patchwork.plot.Rd 2013-01-04 10:24:05 UTC (rev 154)
@@ -36,7 +36,11 @@
\item{Tumor.vcf}{
Default is NULL.
If samtools mpileup command has been used you will need to generate a vcf file using
- samtools mpileup -uf reference.fasta tumor.bam | bcftools view -vcg - > outfile.vcf
+ samtools mpileup -uf reference.fasta tumor.bam | bcftools view -bvcg - > raw.bcf
+ and then
+ bcftools view raw.bcf | vcfutils.pl varFilter -D100 > outfile.vcf
+ Where the -D100 option filters out SNPs with a read depth higher than 100. It should be changed
+ depending on coverage, at 30x -D100 should be ok and at 120x -D500 might be more suitable for example.
}
\item{Normal.bam}{
Default is NULL.
Modified: pkg/patchworkCG/R/patchwork.CG.copynumbers.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.copynumbers.r 2012-11-30 10:54:10 UTC (rev 153)
+++ pkg/patchworkCG/R/patchwork.CG.copynumbers.r 2013-01-04 10:24:05 UTC (rev 154)
@@ -2,14 +2,11 @@
{
data(ideogram,package="patchworkCG")
- if(length(CGfile)==1)
+ if (length(CGfile)==1)
{
load(CGfile)
- }
- else
- {
- load("CG.Rdata")
- }
+ } else { load("CG.Rdata")
+ }
voidchrom <- c('chrX','chrY') # may add non-integer chroms here....
@@ -235,11 +232,15 @@
distance <- Inf
for (cn in 0:maxCn)
{
+ cat("cn: ",cn,"\n")
t_int <- int[paste('cn',cn,sep='')][[1]] ## get Log-R of particular cn from 'int'
+ cat("t_int: ",t_int,"\n")
t_dis <- abs(regions$ratio[i]-t_int) ## distance to that particular cn
+ cat("t_dis: ",t_dis,"\n")
if (t_dis < distance)
{ ## nearest so far, save.
distance <- t_dis -> intDist[i]
+ cat("distance: ",distance,"\n")
Cn[i] <- cn
}
}
@@ -273,8 +274,8 @@
else
{
mCn[i] <- NA
- fullCN[i] <- paste('cn',Cn[i],'m',mCn[i],sep='') # Full description
}
+ fullCN[i] <- paste('cn',Cn[i],'m',mCn[i],sep='') # Full description
}
regions$Cn <- Cn
Modified: pkg/patchworkCG/R/zzz.R
===================================================================
--- pkg/patchworkCG/R/zzz.R 2012-11-30 10:54:10 UTC (rev 153)
+++ pkg/patchworkCG/R/zzz.R 2013-01-04 10:24:05 UTC (rev 154)
@@ -4,8 +4,8 @@
packageStartupMessage("\n")
packageStartupMessage("Version: ",utils::packageDescription('patchworkCG')$Version)
packageStartupMessage("\n")
- packageStartupMessage("If this is your first time, please see the documentation in")
- packageStartupMessage("the README file at the default installation location, the")
- packageStartupMessage("homepage (http://patchwork.r-forge.r-project.org/) or ?patchworkCG.readme")
+ packageStartupMessage("If this is your first time, please see the documentation at the")
+ #packageStartupMessage("the README file at the default installation location, the")
+ packageStartupMessage("homepage (http://patchwork.r-forge.r-project.org/) or in ?patchworkCG.readme")
packageStartupMessage("or the README file found at the install location of patchworkCG/example_plots/README")
}
\ No newline at end of file
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