[Patchwork-commits] r86 - pkg/patchwork/R

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

Author: mayrhofer
Date: 2012-02-09 16:39:20 +0100 (Thu, 09 Feb 2012)
New Revision: 86

Modified:
   pkg/patchwork/R/patchwork.CNA.r
   pkg/patchwork/R/patchwork.alleledata.r
Log:
degubs

Modified: pkg/patchwork/R/patchwork.CNA.r
===================================================================
--- pkg/patchwork/R/patchwork.CNA.r	2012-02-09 15:05:56 UTC (rev 85)
+++ pkg/patchwork/R/patchwork.CNA.r	2012-02-09 15:39:20 UTC (rev 86)
@@ -11,13 +11,13 @@
 	#load(paste(packagepath,"/data/normaldata.RData",sep=""))
 	
 	#Attempt to read file pile.alleles, incase its already been created.
-	alf = NULL
+	alf <- normalalf <- NULL
 	try( load("pile.alleles.Rdata"), silent=TRUE )
 	
 	#If it wasnt created, create it using the perl script pile2alleles.pl
 	#which is included in the package. Creates pile.alleles in whichever folder
 	#you are running R from. (getwd())
-	if(length(alf) == 0)
+	if(is.null(alf))
 		{
 		cat("Initiating Allele Data Generation \n")
 		normalalf <- ifelse(is.null(normal.pileup), NULL, patchwork.alleledata(normal.pileup))

Modified: pkg/patchwork/R/patchwork.alleledata.r
===================================================================
--- pkg/patchwork/R/patchwork.alleledata.r	2012-02-09 15:05:56 UTC (rev 85)
+++ pkg/patchwork/R/patchwork.alleledata.r	2012-02-09 15:39:20 UTC (rev 86)
@@ -54,7 +54,7 @@
 	
 	#Finally, if a matched normal was available, remove SNPs that were not (somewhat) heterozygous there.
 	if (!is.null(normalalf)) {
-		normalalf <- normalalf[normalalf$amin/normalalf$atot > 0.2,]
+		normalalf <- normalalf[normalalf$amin/normalalf$atot > 0.1,]
 		alf <- merge(normalalf[,1:2],alf,by=1:2,all=F)
 	}