[Patchwork-commits] r171 - in pkg: patchwork patchwork/R patchworkCG/man

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

Author: sebastian_d
Date: 2013-06-05 14:18:30 +0200 (Wed, 05 Jun 2013)
New Revision: 171

Modified:
   pkg/patchwork/DESCRIPTION
   pkg/patchwork/R/patchwork.alleledata.r
   pkg/patchworkCG/man/patchwork.CG.plot.Rd
Log:
update that should fix gooch bugg

Modified: pkg/patchwork/DESCRIPTION
===================================================================
--- pkg/patchwork/DESCRIPTION	2013-06-03 12:42:06 UTC (rev 170)
+++ pkg/patchwork/DESCRIPTION	2013-06-05 12:18:30 UTC (rev 171)
@@ -3,9 +3,9 @@
 Title: Allele-specific Copy Number Analysis of whole genome data
 Version: 2.2
 Date: 2012-30-08
-Author: Markus Rasmussen, Sebastian DiLorenzo
-Maintainer: Markus Rasmussen <Markus.Mayrhofer at medsci.uu.se>
-Description: Performs a copy number analysis of whole genome data.
+Author: Markus Mayrhofer, Sebastian DiLorenzo
+Maintainer: Markus Mayrhofer <Markus.Mayrhofer at medsci.uu.se>
+Description: Performs a allele-specific copy number analysis of whole genome data.
 License: GPL-2
 Imports: patchworkData
 Depends: DNAcopy

Modified: pkg/patchwork/R/patchwork.alleledata.r
===================================================================
--- pkg/patchwork/R/patchwork.alleledata.r	2013-06-03 12:42:06 UTC (rev 170)
+++ pkg/patchwork/R/patchwork.alleledata.r	2013-06-05 12:18:30 UTC (rev 171)
@@ -19,16 +19,17 @@
 	#Copy perl information from package install location
 	system(paste("cp -r ",packagepath,"/perl .perl",sep=""))
 
-	if (is.null(vcf)==F)
+	if(is.null(vcf))
 		{
+		#old samtools pileup -vcf used.
+		#cat("pileup used \n")
+		system(paste("cat ",Pileup," | perl .perl/pile2alleles.pl > ",getwd(),"/pile.alleles",sep=""))
+		} else 
+		{
 		#mpileup and bcftools used. read the pileup and vcf.
+		#cat("mpileup used \n")
 		system(paste("perl .perl/mpile2alleles.pl ",Pileup," ",vcf," >",getwd(),"/pile.alleles",sep=""))
 		}
-		else 
-		{
-		#old samtools pileup -vcf used.
-		system(paste("cat ",Pileup," | perl .perl/pile2alleles.pl > ",getwd(),"/pile.alleles",sep=""))
-		}
 
 		#Cleanup
 		system("rm -r .perl")
@@ -48,7 +49,10 @@
 	#Force compatability between naming of chromosomes to our chromosome names
 	#from ideogram file. chr1...chr22,chrX,chrY
 	data(ideogram,package="patchworkData")
-	alf = alf[-grep("M",alf$achr),]
+	if(length(grep("M",alf$achr))!=0)
+		{
+		alf = alf[-grep("M",alf$achr),]
+		}
 	alf$achr = as.character(alf$achr)
 	
 	x_x = strsplit(alf$achr[1],"chr")
@@ -81,8 +85,7 @@
 	if (as.numeric(hgcheck[[1]][2]) <= 10000)
 		{
 		data(commonSnpsHG18,package="patchworkData")
-		}
-	else
+  } else
 		{
 		data(commonSnps132,package="patchworkData")
 		}

Modified: pkg/patchworkCG/man/patchwork.CG.plot.Rd
===================================================================
--- pkg/patchworkCG/man/patchwork.CG.plot.Rd	2013-06-03 12:42:06 UTC (rev 170)
+++ pkg/patchworkCG/man/patchwork.CG.plot.Rd	2013-06-05 12:18:30 UTC (rev 171)
@@ -22,7 +22,8 @@
 
 \arguments{
   \item{path}{
-  	Path to the ASM folder. One of the subfolders of your completegenomics directory.
+  	Path to the ASM folder. One of the subfolders of your completegenomics directory. Should be given as a string.
+    Ex. path="path/to/ASM".
 	}
   \item{name}{
 	Default is 'CG_sample'. The name you wish associated with the plots that will be generated.