[Patchwork-commits] r55 - in pkg/patchwork: . R man

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

Author: sebastian_d
Date: 2011-12-14 16:23:19 +0100 (Wed, 14 Dec 2011)
New Revision: 55

Modified:
   pkg/patchwork/DESCRIPTION
   pkg/patchwork/R/patchwork.readChroms.r
   pkg/patchwork/man/karyotype.Rd
   pkg/patchwork/man/karyotype_chroms.Rd
   pkg/patchwork/man/patchwork.findCNs.Rd
Log:
some small fixes to get the new data system working

Modified: pkg/patchwork/DESCRIPTION
===================================================================
--- pkg/patchwork/DESCRIPTION	2011-12-14 14:23:48 UTC (rev 54)
+++ pkg/patchwork/DESCRIPTION	2011-12-14 15:23:19 UTC (rev 55)
@@ -7,5 +7,4 @@
 Maintainer: Markus Rasmussen <Markus.Rasmussen at medsci.uu.se>
 Description: Performs a copy number analysis of whole genome data.
 License: GPL-2
-LazyLoad: no
 Imports: DNAcopy,patchworkData

Modified: pkg/patchwork/R/patchwork.readChroms.r
===================================================================
--- pkg/patchwork/R/patchwork.readChroms.r	2011-12-14 14:23:48 UTC (rev 54)
+++ pkg/patchwork/R/patchwork.readChroms.r	2011-12-14 15:23:19 UTC (rev 55)
@@ -52,7 +52,6 @@
 	readlength=80 # this is currently hard coded and may be adjusted.
 	seglength=200 # (do not change)
 	data=NULL
-	tmp = NULL
 
 	for (c in chroms) 
 		{
@@ -62,8 +61,7 @@
 		system(paste("python .python/Pysamloader.py ",BamFile," ",c,sep =""))
 		# Load the newly created position file
 		unix = read.csv(".Tmp_chr_pos",sep='',header=F)$V1 + readlength/2
-		tmp = paste(c,".mark",sep="")
-		load(paste(datapath,"/data/",c,".mark.RData",sep=""))
+		gc = readRDS(paste(datapath,"/extdata/",c,".mark.rds",sep=""))
 		xpos=gc[,1]
 		xgc=gc[,2]
 		xgck=gc[,3]

Modified: pkg/patchwork/man/karyotype.Rd
===================================================================
--- pkg/patchwork/man/karyotype.Rd	2011-12-14 14:23:48 UTC (rev 54)
+++ pkg/patchwork/man/karyotype.Rd	2011-12-14 15:23:19 UTC (rev 55)
@@ -12,7 +12,7 @@
 }
 
 \usage{
-karyotype(chr,start,end,int,ai,chroms,name,xlim,ylim)
+karyotype(chr,start,end,int,ai,name,xlim,ylim)
 }
 
 \arguments{
@@ -31,9 +31,6 @@
 	\item{ai}{					%segs$ai
   	Allelic imbalance.
 	}
-	\item{chroms}{
-  	Object created in patchwork.CNA which holds chromosome names.
-	}
 	\item{name}{
   	Default is the name of the input BamFile from patchwork.CNA().
   	Plot generated as "name.karyotype.png" in your working directory.

Modified: pkg/patchwork/man/karyotype_chroms.Rd
===================================================================
--- pkg/patchwork/man/karyotype_chroms.Rd	2011-12-14 14:23:48 UTC (rev 54)
+++ pkg/patchwork/man/karyotype_chroms.Rd	2011-12-14 15:23:19 UTC (rev 55)
@@ -12,7 +12,7 @@
 }
 
 \usage{
-karyotype_chroms(chr,start,end,int,ai,chroms,mchr,mpos,mval,schr,spos,sval,name,xlim,ylim)
+karyotype_chroms(chr,start,end,int,ai,mchr,mpos,mval,schr,spos,sval,name,xlim,ylim)
 }
 
 \arguments{
@@ -31,9 +31,6 @@
 	\item{ai}{					%segs$ai
   	Allelic imbalance.
 	}
-	\item{chroms}{
-  	Object created in patchwork.CNA which holds chromosome names.
-	}
 	\item{mchr}{
 	Chromosomes name of kbsegs object. Final version of kbsegs created from patchwork.smoothing().
 	}

Modified: pkg/patchwork/man/patchwork.findCNs.Rd
===================================================================
--- pkg/patchwork/man/patchwork.findCNs.Rd	2011-12-14 14:23:48 UTC (rev 54)
+++ pkg/patchwork/man/patchwork.findCNs.Rd	2011-12-14 15:23:19 UTC (rev 55)
@@ -73,8 +73,8 @@
 %% ~Make other sections like Warning with \section{Warning }{....} ~
 
 \seealso{
-\code{\link{patchwork.CNA}} \cr
-\code{\link{subfunctions_findCNs}}
+\code{\link[patchwork]{patchwork.CNA}} \cr
+\code{\link[patchwork]{subfunctions_findCNs}}
 }
 
 %\examples{