[Patchwork-commits] r79 - in pkg/patchworkCG: . R

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

Author: sebastian_d
Date: 2012-02-06 17:13:29 +0100 (Mon, 06 Feb 2012)
New Revision: 79

Modified:
   pkg/patchworkCG/NAMESPACE
   pkg/patchworkCG/R/patchwork.CG.r
   pkg/patchworkCG/R/patchwork.CGCNV.r
Log:
Some spring cleaning

Modified: pkg/patchworkCG/NAMESPACE
===================================================================
--- pkg/patchworkCG/NAMESPACE	2012-02-06 16:05:26 UTC (rev 78)
+++ pkg/patchworkCG/NAMESPACE	2012-02-06 16:13:29 UTC (rev 79)
@@ -1,5 +1,4 @@
-export(patchwork.AI,
-		patchwork.CG,
+export(patchwork.CG,
 		CG_Ka_check,
 		CG_KaCh,
 		CG_KaChCN,

Modified: pkg/patchworkCG/R/patchwork.CG.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.r	2012-02-06 16:05:26 UTC (rev 78)
+++ pkg/patchworkCG/R/patchwork.CG.r	2012-02-06 16:13:29 UTC (rev 79)
@@ -219,22 +219,6 @@
 	#Remove NA values generated by for example 0/0
 	mastervar = mastervar[!is.na(mastervar[,8]),]
 
-	#only keep stuff in column 4 that is snp
-	#mastervar = mastervar[mastervar$vartype == "snp",]
-	#norm_mv = norm_mv[norm_mv$vartype == "snp",]
-	
-	#remove all NA values. (there are no reads on that position)
-	#mastervar = mastervar[!is.na(mastervar[,6]),]
-
-	#ix = mastervar$ref_count < 3 | mastervar$ref_count == 0 | mastervar$ref_count == mastervar$tot_count
-	#mastervar = mastervar[!ix,]
-	
-	#ix = mastervar$ref_count == 0
-	#mastervar = mastervar[!ix,]
-	
-	#ix = mastervar$ref_count == mastervar$tot_count
-	#mastervar = mastervar[!ix,]
-	
 	#------------------------------------------------#
 	# Add and calculate some columns for mastervar
 	#------------------------------------------------#

Modified: pkg/patchworkCG/R/patchwork.CGCNV.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CGCNV.r	2012-02-06 16:05:26 UTC (rev 78)
+++ pkg/patchworkCG/R/patchwork.CGCNV.r	2012-02-06 16:13:29 UTC (rev 79)
@@ -1,9 +1,5 @@
 patchwork.CGCNV = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV_",CGfile=NULL)
 	{
-	# patchwork.CGCNV(0.75,0.35,0.25,0.95)
-	#packagepath = system.file(package="patchwork")
-	#load(paste(packagepath,"/data/commonSnps132.RData",sep=""))
-	#load(paste(packagepath,"/data/ideogram.RData",sep=""))
 	data(ideogram,package="patchworkCG")
 	
 	if(length(CGfile)==1)