[Patchwork-commits] r78 - in pkg/patchworkCG: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 6 17:05:26 CET 2012
Author: sebastian_d
Date: 2012-02-06 17:05:26 +0100 (Mon, 06 Feb 2012)
New Revision: 78
Removed:
pkg/patchworkCG/R/patchwork.AI.r
pkg/patchworkCG/man/patchwork.AI.Rd
Modified:
pkg/patchworkCG/R/patchwork.CG.r
pkg/patchworkCG/man/CG_KaCh.Rd
pkg/patchworkCG/man/CG_KaChCN.Rd
pkg/patchworkCG/man/CG_karyotype.Rd
pkg/patchworkCG/man/subfunctions_CGCNV.Rd
Log:
removed patchworkAI
Deleted: pkg/patchworkCG/R/patchwork.AI.r
===================================================================
--- pkg/patchworkCG/R/patchwork.AI.r 2012-02-02 08:31:28 UTC (rev 77)
+++ pkg/patchworkCG/R/patchwork.AI.r 2012-02-06 16:05:26 UTC (rev 78)
@@ -1,20 +0,0 @@
-patchwork.AI <- function(segs,mastervar)
- {
- segs$ai <- segs$snvs <- segs$ratio <- NA
-
- for (i in 1:nrow(segs))
- {
- #Calculate ratio between relcov and segment lengths
- segs$ratio[i] = segs$relcov[i] / (sum(as.numeric(segs$relcov*(segs$end-segs$start))) / sum(as.numeric(segs$end - segs$start)))
-
- #Index of correct snp positions to pull snp data from
- # right chromosome
- ix = mastervar$chr==as.character(segs$chr[i]) &
- # right area (between start and end)
- (mastervar$begin > segs$start[i] & mastervar$begin < segs$end[i])
- segs$snvs[i] = sum(ix)
- segs$ai[i] = 1 - sum(mastervar$min[ix]) / sum(mastervar$max[ix])
- }
- segs$ai[is.nan(segs$ai)]=0
- return(segs)
- }
\ No newline at end of file
Modified: pkg/patchworkCG/R/patchwork.CG.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.r 2012-02-02 08:31:28 UTC (rev 77)
+++ pkg/patchworkCG/R/patchwork.CG.r 2012-02-06 16:05:26 UTC (rev 78)
@@ -253,18 +253,32 @@
mastervar$max = apply(mastervar[,c(5,9)],1,max)
mastervar$min = mastervar$tot_count - mastervar$max
mastervar$ratio = mastervar$tot_count / mean(mastervar$tot_count)
+
+ segm = patchwork.AI(segm,mastervar)
- #------------------------------------------------#
- # Create segs using patchwork.AI, save files
- #------------------------------------------------#
+ segm$ai <- segm$snvs <- segm$ratio <- NA
- segs = patchwork.AI(segm,mastervar)
+ #Generate the allelic imbalance calculation, among other things.
+ for (i in 1:nrow(segm))
+ {
+ #Calculate ratio between relcov and segment lengths
+ segm$ratio[i] = segm$relcov[i] / (sum(as.numeric(segm$relcov*(segm$end-segm$start))) / sum(as.numeric(segm$end - segm$start)))
+
+ #Index of correct snp positions to pull snp data from
+ # right chromosome
+ ix = mastervar$chr==as.character(segm$chr[i]) &
+ # right area (between start and end)
+ (mastervar$begin > segm$start[i] & mastervar$begin < segm$end[i])
+ segm$snvs[i] = sum(ix)
+ segm$ai[i] = 1 - sum(mastervar$min[ix]) / sum(mastervar$max[ix])
+ }
+ segm$ai[is.nan(segm$ai)]=0
cat("Calculations complete \n")
cat("Saving objects to CG.Rdata \n")
- save(segs,mastervar,depcov,file="CG.Rdata")
+ save(segm,mastervar,depcov,file="CG.Rdata")
#------------------------------------------------#
# Plot
@@ -272,10 +286,10 @@
cat("Initiating Plotting \n")
- CG_karyotype(segs$chr,segs$start,segs$end,segs$ratio,segs$ai,
+ CG_karyotype(segm$chr,segm$start,segm$end,segm$ratio,segm$ai,
name=name,xlim=c(0,2.4),ylim=c(0,1))
- CG_KaCh(segs$chr,segs$start,segs$end,segs$ratio,segs$ai,
+ CG_KaCh(segm$chr,segm$start,segm$end,segm$ratio,segm$ai,
depcov$chr,depcov$begin,depcov$ratio,(1 - mastervar$min/mastervar$max),
mastervar$chr,mastervar$begin,
name=name,xlim=c(0,2.4),ylim=c(0,1))
Modified: pkg/patchworkCG/man/CG_KaCh.Rd
===================================================================
--- pkg/patchworkCG/man/CG_KaCh.Rd 2012-02-02 08:31:28 UTC (rev 77)
+++ pkg/patchworkCG/man/CG_KaCh.Rd 2012-02-06 16:05:26 UTC (rev 78)
@@ -17,8 +17,7 @@
\arguments{
\item{chr}{
- Chromosomes name of segs object, as generated from somaticCnvSegmentsNonDiplod file.
- Final version of segs created in patchwork.AI().
+ Chromosomes name of segm object, as generated from somaticCnvSegmentsNonDiplod file.
}
\item{start}{
Start position of segment.
Modified: pkg/patchworkCG/man/CG_KaChCN.Rd
===================================================================
--- pkg/patchworkCG/man/CG_KaChCN.Rd 2012-02-02 08:31:28 UTC (rev 77)
+++ pkg/patchworkCG/man/CG_KaChCN.Rd 2012-02-06 16:05:26 UTC (rev 78)
@@ -18,7 +18,7 @@
\arguments{
\item{chr}{
- Chromosomes name of segs object. Final version of segs created from patchwork.AI().
+ Chromosomes name of segm object.
}
\item{start}{
Start position of segment.
Modified: pkg/patchworkCG/man/CG_karyotype.Rd
===================================================================
--- pkg/patchworkCG/man/CG_karyotype.Rd 2012-02-02 08:31:28 UTC (rev 77)
+++ pkg/patchworkCG/man/CG_karyotype.Rd 2012-02-06 16:05:26 UTC (rev 78)
@@ -17,8 +17,7 @@
\arguments{
\item{chr}{
- Chromosomes name of segs object, as generated from somaticCnvSegmentsNonDiplod file.
- Final version of segs created in patchwork.AI().
+ Chromosomes name of segm object, as generated from somaticCnvSegmentsNonDiplod file.
}
\item{start}{
Start position of segment.
Deleted: pkg/patchworkCG/man/patchwork.AI.Rd
===================================================================
--- pkg/patchworkCG/man/patchwork.AI.Rd 2012-02-02 08:31:28 UTC (rev 77)
+++ pkg/patchworkCG/man/patchwork.AI.Rd 2012-02-06 16:05:26 UTC (rev 78)
@@ -1,70 +0,0 @@
-\name{patchwork.AI}
-\alias{patchwork.AI}
-\alias{AI}
-
-
-\title{
-Function to calculate Allelic Imbalance
-}
-
-\description{
-Generates the segs object, internal function within patchwork.CG().
-}
-
-\usage{
-patchwork.AI(segs,mastervar)
-}
-
-\arguments{
- \item{segs}{
- This object is initially read from the somaticCnvSegmentsNondiploidBeta file in the CNV directory
- of your CompleteGenomics data.
- }
- \item{mastervar}{
- This object is initially read then edited from the masterVarBeta file in the ASM directory
- of your CompleteGenomics data.
- }
-}
-
-\details{
-As this is an internal function it is mostly there to keep the code clean. It is not recommended
-that this function be run except as it was intended in patchwork.CG().
-}
-
-%\value{
-%% ~Describe the value returned
-%% If it is a LIST, use
-%% \item{comp1 }{Description of 'comp1'}
-%% \item{comp2 }{Description of 'comp2'}
-%% ...
-%}
-
-%\references{
-%% ~put references to the literature/web site here ~
-%}
-
-\author{
-Markus Mayrhofer, \email{markus.mayrhofer at medsci.uu.se} \cr
-Sebastian DiLorenzo, \email{sebastian.dilorenzo at medsci.uu.se}
-}
-%\note{
-%% ~~further notes~~
-%}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-\code{\link{patchwork.CG}}
-}
-
-%\examples{
-%##---- Should be DIRECTLY executable !! ----
-%##-- ==> Define data, use random,
-%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
-%}
-
-% Add one or more standard keywords, see file 'KEYWORDS' in the
-% R documentation directory.
-%\keyword{ ~kwd1 }
-%\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
\ No newline at end of file
Modified: pkg/patchworkCG/man/subfunctions_CGCNV.Rd
===================================================================
--- pkg/patchworkCG/man/subfunctions_CGCNV.Rd 2012-02-02 08:31:28 UTC (rev 77)
+++ pkg/patchworkCG/man/subfunctions_CGCNV.Rd 2012-02-06 16:05:26 UTC (rev 78)
@@ -39,7 +39,7 @@
Weights to be applied.
}
\item{vector}{
- The segs objects chr column.
+ The segm objects chr column.
}
}
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