[Patchwork-commits] r30 - in pkg/patchwork: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Nov 25 16:59:13 CET 2011
Author: sebastian_d
Date: 2011-11-25 16:59:12 +0100 (Fri, 25 Nov 2011)
New Revision: 30
Modified:
pkg/patchwork/DESCRIPTION
pkg/patchwork/NAMESPACE
pkg/patchwork/R/karyotype_check.r
pkg/patchwork/R/patchwork.CNA.r
pkg/patchwork/R/patchwork.applyref.r
pkg/patchwork/R/patchwork.findCNs.r
pkg/patchwork/R/patchwork.segment.r
pkg/patchwork/man/chr1.mark.Rd
pkg/patchwork/man/chr10.mark.Rd
pkg/patchwork/man/chr11.mark.Rd
pkg/patchwork/man/chr12.mark.Rd
pkg/patchwork/man/chr13.mark.Rd
pkg/patchwork/man/chr14.mark.Rd
pkg/patchwork/man/chr15.mark.Rd
pkg/patchwork/man/chr16.mark.Rd
pkg/patchwork/man/chr17.mark.Rd
pkg/patchwork/man/chr18.mark.Rd
pkg/patchwork/man/chr19.mark.Rd
pkg/patchwork/man/chr2.mark.Rd
pkg/patchwork/man/chr20.mark.Rd
pkg/patchwork/man/chr21.mark.Rd
pkg/patchwork/man/chr22.mark.Rd
pkg/patchwork/man/chr3.mark.Rd
pkg/patchwork/man/chr4.mark.Rd
pkg/patchwork/man/chr5.mark.Rd
pkg/patchwork/man/chr6.mark.Rd
pkg/patchwork/man/chr7.mark.Rd
pkg/patchwork/man/chr8.mark.Rd
pkg/patchwork/man/chr9.mark.Rd
pkg/patchwork/man/chrX.mark.Rd
pkg/patchwork/man/chrY.mark.Rd
pkg/patchwork/man/commonSnps132.Rd
pkg/patchwork/man/datasolexa.Rd
pkg/patchwork/man/datasolid.Rd
pkg/patchwork/man/karyotype_check.Rd
Log:
Pre weekend commit ;)
Modified: pkg/patchwork/DESCRIPTION
===================================================================
--- pkg/patchwork/DESCRIPTION 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/DESCRIPTION 2011-11-25 15:59:12 UTC (rev 30)
@@ -8,3 +8,6 @@
Description: Performs a copy number analysis of whole genome data.
License: GPL-2
LazyLoad: no
+#LazyData: yes
+Depends: DNAcopy
+Imports: DNAcopy
Modified: pkg/patchwork/NAMESPACE
===================================================================
--- pkg/patchwork/NAMESPACE 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/NAMESPACE 2011-11-25 15:59:12 UTC (rev 30)
@@ -5,15 +5,18 @@
patchwork.alleledata,
patchwork.applyref,
patchwork.CNA,
+ patchwork.createreference,
+ patchwork.findCNs,
patchwork.GCNorm,
patchwork.Medians_n_AI,
patchwork.readChroms,
patchwork.segment,
patchwork.smoothing,
- patchwork.createreference,
+ #subfunctions_findCNs
weightedMedian,
weightedMean,
is.autosome,
deChrom_ucsc,
- chrom_ucsc,
- patchwork.findCNs)
\ No newline at end of file
+ chrom_ucsc)
+
+imports(DNAcopy)
\ No newline at end of file
Modified: pkg/patchwork/R/karyotype_check.r
===================================================================
--- pkg/patchwork/R/karyotype_check.r 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/R/karyotype_check.r 2011-11-25 15:59:12 UTC (rev 30)
@@ -1,11 +1,9 @@
-karyotype_check <- function(chr,start,end,int,ai,Cn,mCn,t,ideogram=NULL,name='',xlim=c(-1.02,1.02),ylim=0:1)
+karyotype_check <- function(chr,start,end,int,ai,Cn,mCn,t,name='',xlim=c(-1.02,1.02),ylim=0:1)
{
## TAPS scatter plot of a full sample, used for visual quality control.
png(paste(name,'_karyotype_check.png',sep=''),width=1300,height=1300)
- packagepath = system.file(package="patchwork")
-
- load(paste(packagepath,"/data/ideogram.RData",sep=""))
+
colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
Modified: pkg/patchwork/R/patchwork.CNA.r
===================================================================
--- pkg/patchwork/R/patchwork.CNA.r 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/R/patchwork.CNA.r 2011-11-25 15:59:12 UTC (rev 30)
@@ -86,7 +86,7 @@
cat("Segment data extraction Complete \n \n \n")
cat("Saving information objects needed for patchwork.findCNs in findCNs.Rdata \n \n \n")
- save(segs,alf,kbsegs,file="findCNs.Rdata")
+ save(segs,alf,kbsegs,BamFile,file="findCNs.Rdata")
#Plot it
cat("Initiating Plotting \n")
Modified: pkg/patchwork/R/patchwork.applyref.r
===================================================================
--- pkg/patchwork/R/patchwork.applyref.r 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/R/patchwork.applyref.r 2011-11-25 15:59:12 UTC (rev 30)
@@ -1,9 +1,5 @@
patchwork.applyref <- function(data,reference)
{
-
- #This load shall be changed to read Illumina data as default
- #and SOLiD if choosen.
-
#Load data included in package
packagepath = system.file(package="patchwork")
#load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
@@ -13,7 +9,8 @@
{
load(paste(packagepath,"/data/datasolid.RData",sep=""))
normaldata = datasolid
- ifelse(tolower(reference) %in% c("solexa","illumina"))
+ }
+ else if(tolower(reference) %in% c("solexa","illumina"))
{
load(paste(packagepath,"/data/datasolexa.RData",sep=""))
normaldata = datasolexa
Modified: pkg/patchwork/R/patchwork.findCNs.r
===================================================================
--- pkg/patchwork/R/patchwork.findCNs.r 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/R/patchwork.findCNs.r 2011-11-25 15:59:12 UTC (rev 30)
@@ -270,6 +270,13 @@
tumor_percent <- xdelta / expected_delta
- karyotype_check(regions$chr,regions$start,regions$end,regions$mean,regions$ai,regions$Cn,regions$mCn,list(int=int,ai=ai),ideogram=NULL,name='',xlim=c(0,2.4),ylim=c(0.3,1))
- karyotype_chromsCN(regions$chr,regions$start,regions$end,regions$mean,regions$ai,regions$Cn,regions$mCn,ideogram=ideogram,kbsegs$chr,kbsegs$pos,kbsegs$ratio,alf$achr,alf$apos,(1-alf$amin/alf$amax),name='TAPSeq',xlim=c(0,2.4),ylim=c(0.3,1))
+ karyotype_check(regions$chr,regions$start,regions$end,regions$mean,regions$ai,
+ regions$Cn,regions$mCn,list(int=int,ai=ai),name=as.character(BamFile),
+ xlim=c(0,2.4),ylim=c(0.3,1))
+
+ karyotype_chromsCN(regions$chr,regions$start,regions$end,regions$mean,regions$ai,
+ regions$Cn,regions$mCn,ideogram=ideogram,kbsegs$chr,
+ kbsegs$pos,kbsegs$ratio,alf$achr,alf$apos,
+ (1-alf$amin/alf$amax),name=as.character(BamFile),xlim=c(0,2.4),
+ ylim=c(0.3,1))
}
\ No newline at end of file
Modified: pkg/patchwork/R/patchwork.segment.r
===================================================================
--- pkg/patchwork/R/patchwork.segment.r 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/R/patchwork.segment.r 2011-11-25 15:59:12 UTC (rev 30)
@@ -1,6 +1,6 @@
patchwork.segment <- function(kbsegs,chroms,Alpha,SD)
{
- library(DNAcopy)
+ #library(DNAcopy)
#Load data included in package
packagepath = system.file(package="patchwork")
#load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
Modified: pkg/patchwork/man/chr1.mark.Rd
===================================================================
--- pkg/patchwork/man/chr1.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr1.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr1.mark,package="patchwork")}
+\usage{chr1.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr10.mark.Rd
===================================================================
--- pkg/patchwork/man/chr10.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr10.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr10.mark,package="patchwork")}
+\usage{chr10.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr11.mark.Rd
===================================================================
--- pkg/patchwork/man/chr11.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr11.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr11.mark,package="patchwork")}
+\usage{chr11.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr12.mark.Rd
===================================================================
--- pkg/patchwork/man/chr12.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr12.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr12.mark,package="patchwork")}
+\usage{chr12.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr13.mark.Rd
===================================================================
--- pkg/patchwork/man/chr13.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr13.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr13.mark,package="patchwork")}
+\usage{chr13.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr14.mark.Rd
===================================================================
--- pkg/patchwork/man/chr14.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr14.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr14.mark,package="patchwork")}
+\usage{chr14.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr15.mark.Rd
===================================================================
--- pkg/patchwork/man/chr15.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr15.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr15.mark,package="patchwork")}
+\usage{chr15.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr16.mark.Rd
===================================================================
--- pkg/patchwork/man/chr16.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr16.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr16.mark,package="patchwork")}
+\usage{chr16.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr17.mark.Rd
===================================================================
--- pkg/patchwork/man/chr17.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr17.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr17.mark,package="patchwork")}
+\usage{chr17.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr18.mark.Rd
===================================================================
--- pkg/patchwork/man/chr18.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr18.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr18.mark,package="patchwork")}
+\usage{chr18.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr19.mark.Rd
===================================================================
--- pkg/patchwork/man/chr19.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr19.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr19.mark,package="patchwork")}
+\usage{chr19.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr2.mark.Rd
===================================================================
--- pkg/patchwork/man/chr2.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr2.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr2.mark,package="patchwork")}
+\usage{chr2.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr20.mark.Rd
===================================================================
--- pkg/patchwork/man/chr20.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr20.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr20.mark,package="patchwork")}
+\usage{chr20.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr21.mark.Rd
===================================================================
--- pkg/patchwork/man/chr21.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr21.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr21.mark,package="patchwork")}
+\usage{chr21.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr22.mark.Rd
===================================================================
--- pkg/patchwork/man/chr22.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr22.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr22.mark,package="patchwork")}
+\usage{chr22.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr3.mark.Rd
===================================================================
--- pkg/patchwork/man/chr3.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr3.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr3.mark,package="patchwork")}
+\usage{chr3.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr4.mark.Rd
===================================================================
--- pkg/patchwork/man/chr4.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr4.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr4.mark,package="patchwork")}
+\usage{chr4.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr5.mark.Rd
===================================================================
--- pkg/patchwork/man/chr5.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr5.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr5.mark,package="patchwork")}
+\usage{chr5.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr6.mark.Rd
===================================================================
--- pkg/patchwork/man/chr6.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr6.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr6.mark,package="patchwork")}
+\usage{chr6.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr7.mark.Rd
===================================================================
--- pkg/patchwork/man/chr7.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr7.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr7.mark,package="patchwork")}
+\usage{chr7.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr8.mark.Rd
===================================================================
--- pkg/patchwork/man/chr8.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr8.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr8.mark,package="patchwork")}
+\usage{chr8.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chr9.mark.Rd
===================================================================
--- pkg/patchwork/man/chr9.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chr9.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chr9.mark,package="patchwork")}
+\usage{chr9.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chrX.mark.Rd
===================================================================
--- pkg/patchwork/man/chrX.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chrX.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chrX.mark,package="patchwork")}
+\usage{chrX.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/chrY.mark.Rd
===================================================================
--- pkg/patchwork/man/chrY.mark.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/chrY.mark.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(chrY.mark,package="patchwork")}
+\usage{chrY.mark}
\format{
A data frame with the following 4 variables.
Modified: pkg/patchwork/man/commonSnps132.Rd
===================================================================
--- pkg/patchwork/man/commonSnps132.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/commonSnps132.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,7 +11,7 @@
}
-\usage{data(commonSnps132,package="patchwork")}
+\usage{commonSnps132}
\format{
A data frame with the following 3 variables.
Modified: pkg/patchwork/man/datasolexa.Rd
===================================================================
--- pkg/patchwork/man/datasolexa.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/datasolexa.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,17 +11,13 @@
}
-\usage{data(datasolexa,package="patchwork")}
+\usage{datasolexa}
\format{
- A data frame with the following 7 variables.
+ A data frame with the following 3 columns.
\describe{
\item{chr}{Which chromosome}
\item{pos}{Position on chromosome}
- \item{gc}{Total GC over 250 base window}
- \item{gck}{Total GC over 1000 base window}
- \item{gcm}{Total GC over million base window}
- \item{counts_mean}{Mean of total read counts. Not used.}
\item{norm_mean}{Mean of normalized coverage}
}
}
Modified: pkg/patchwork/man/datasolid.Rd
===================================================================
--- pkg/patchwork/man/datasolid.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/datasolid.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -11,17 +11,13 @@
}
-\usage{data(datasolid,package="patchwork")}
+\usage{datasolid}
\format{
- A data frame with the following 7 variables.
+ A data frame with the following 3 columns.
\describe{
\item{chr}{Which chromosome}
\item{pos}{Position on chromosome}
- \item{gc}{Total GC over 250 base window}
- \item{gck}{Total GC over 1000 base window}
- \item{gcm}{Total GC over million base window}
- \item{counts_mean}{Mean of total read counts. Not used.}
\item{norm_mean}{Mean of normalized coverage}
}
}
Modified: pkg/patchwork/man/karyotype_check.Rd
===================================================================
--- pkg/patchwork/man/karyotype_check.Rd 2011-11-25 12:52:42 UTC (rev 29)
+++ pkg/patchwork/man/karyotype_check.Rd 2011-11-25 15:59:12 UTC (rev 30)
@@ -4,28 +4,58 @@
\title{
-karyotype checker function
+Karyotype check function
}
\description{
-description
+Plots the whole genome coverage vs allelic imbalance with the approximated
+areas copynumbers and allele constitution. Karyotype_check is called from
+patchwork.findCNs function.
}
\usage{
-karyotype_check(chr,start,end,int,ai,ideogram,name,xlim,ylim)
+karyotype_check(chr,start,end,int,ai,Cn,mCn,t,ideogram=NULL,name='',xlim=c(-1.02,1.02),ylim=0:1)
}
\arguments{
- \item{name}{
- description
+ \item{chr}{ %segs$chr
+ Chromosome.
}
- \item{name2}{
- description
+ \item{start}{ %segs$start
+ Start position of segment.
}
+ \item{end}{ %segs$end
+ End position of segment.
+ }
+ \item{int}{ %segs$mean
+ Mean.
+ }
+ \item{ai}{ %segs$ai
+ Allelic imbalance.
+ }
+ \item{Cn}{
+ Copy number.
+ }
+ \item{mCn}{
+ mCn.
+ }
+ \item{t}{
+ A list between int and ai.
+ }
+ \item{name}{
+ Default is BamFile argument from patchwork.CNA is used as argument.
+ }
+ \item{xlim}{
+ Default is c(0,2.4). Limit of x axis.
+ }
+ \item{ylim}{
+ Default is c(0.3,1). Limit of y axis.
+ }
}
\details{
-Details
+Run within patchwork.findCNs function. findCNs.Rdata must be in working directory for that function
+to run, and thus this one aswell as most of its input is taken from segs.
}
%\value{
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