[Patchwork-commits] r29 - in pkg/patchwork: . R man

[noreply at r-forge.r-project.org]

Author: sebastian_d
Date: 2011-11-25 13:52:42 +0100 (Fri, 25 Nov 2011)
New Revision: 29

Removed:
   pkg/patchwork/R/patchwork.customsegment.r
   pkg/patchwork/man/patchwork.customsegment.Rd
Modified:
   pkg/patchwork/NAMESPACE
Log:
removed customsegment

Modified: pkg/patchwork/NAMESPACE
===================================================================
--- pkg/patchwork/NAMESPACE	2011-11-25 12:50:34 UTC (rev 28)
+++ pkg/patchwork/NAMESPACE	2011-11-25 12:52:42 UTC (rev 29)
@@ -11,7 +11,6 @@
 		patchwork.segment,
 		patchwork.smoothing,
 		patchwork.createreference,
-		patchwork.customsegment,
 		weightedMedian,
 		weightedMean,
 		is.autosome,

Deleted: pkg/patchwork/R/patchwork.customsegment.r
===================================================================
--- pkg/patchwork/R/patchwork.customsegment.r	2011-11-25 12:50:34 UTC (rev 28)
+++ pkg/patchwork/R/patchwork.customsegment.r	2011-11-25 12:52:42 UTC (rev 29)
@@ -1,35 +0,0 @@
-patchwork.customsegment = function(Alpha = 0.0001,SD=1)
-	{
-	#Load DNAcopy
-	library(DNAcopy)
-	#Load data included in package
-	packagepath = system.file(package="patchwork")
-	#load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
-	load(paste(packagepath,"/data/ideogram.RData",sep=""))
-	#load(paste(packagepath,"/data/normaldata.RData",sep=""))
-	load("pile.alleles.Rdata")
-	chroms=as.character(unique(ideogram$chr))
-	load("smoothed.Rdata")
-	
-	# Segmentation
-	segs <- allsegs <- NULL;
-	for (c in chroms)
-		{
-		psegments <- qsegments <- NULL
-		ix= kbsegs$chr==c & kbsegs$pos < ideogram$start[ideogram$chr==c]
-		if (sum(ix)>0)
-			{ 
-			psegments=segment(smooth.CNA(CNA(kbsegs$ratio[ix], c, kbsegs$pos[ix], data.type='logratio',sampleid=paste(c,'p')),smooth.region=40), undo.splits='sdundo', undo.SD=SD,min.width=5, alpha=Alpha)$output[,2:6]
-			psegments$arm='p'
-			}
-		ix=kbsegs$chr==c & kbsegs$pos > ideogram$end[ideogram$chr==c]
-		if (sum(ix)>0)
-			{ 
-			qsegments=segment(smooth.CNA(CNA(kbsegs$ratio[ix], c, kbsegs$pos[ix], data.type='logratio',sampleid=paste(c,'q')),smooth.region=40), undo.splits='sdundo', undo.SD=SD,min.width=5, alpha=Alpha)$output[,2:6]
-			qsegments$arm='q'
-			}
-		segs=rbind(segs,psegments,qsegments)
-		}	
-	colnames(segs)=c('chr','start','end','np','mean','arm')
-	return(segs)
-	}
\ No newline at end of file

Deleted: pkg/patchwork/man/patchwork.customsegment.Rd
===================================================================
--- pkg/patchwork/man/patchwork.customsegment.Rd	2011-11-25 12:50:34 UTC (rev 28)
+++ pkg/patchwork/man/patchwork.customsegment.Rd	2011-11-25 12:52:42 UTC (rev 29)
@@ -1,79 +0,0 @@
-\name{patchwork.customsegment}
-\alias{customsegment}
-\alias{patchwork.customsegment}
-
-
-\title{
-patchworks function for applying custom values to DNAcopy segmentation
-}
-
-\description{
-Using this function you can send the kbsegs object, which is your data
-pre segmentation, and perform a custom segmentation applying your own
-undo.SD and alpha values.
-}
-
-\usage{
-patchwork.customsegment(kbsegs,Alpha = 0.0001,SD = 1)
-}
-
-\arguments{
-  \item{kbsegs}{
-  	The kbsegs object obtained after smoothing in the main CNA function.
-  	If you have run through the code with your data it should be saved in
-  	"smoothing.Rdata". Check your workspace.
-	}
-  \item{Alpha}{
-	Significance levels for the test to accept change-points.
-	}
-  \item{SD}{
-	Reflects undo.SD in DNAcopy segment. The number of Standard Deviations
-	between means to keep a split. Reliant on undo.splits="sdundo".
-	}
-	
-}
-
-\details{
-It is possible to enter the code and change even more values of the segmentation
-but these two were chosen to not clutter and overcomplicate the function
-as they are usually the parameters with most impact.
-}
-
-%\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 Rasmussen
-Sebastian DiLorenzo
-}
-%\note{
-%%  ~~further notes~~
-%}
-
-%% ~Make other sections like Warning with \section{Warning }{....} ~
-
-\seealso{
-\code{\link{patchwork.segment}}
-\code{\link{patchwork.CNA}}
-}
-
-%\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