[Patchwork-commits] r156 - pkg/patchwork/R www

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

Author: sebastian_d
Date: 2013-01-21 13:12:34 +0100 (Mon, 21 Jan 2013)
New Revision: 156

Modified:
   pkg/patchwork/R/patchwork.plot.r
   www/pw_exec.php
Log:
uncomment line to generate normalalf

Modified: pkg/patchwork/R/patchwork.plot.r
===================================================================
--- pkg/patchwork/R/patchwork.plot.r	2013-01-04 10:48:00 UTC (rev 155)
+++ pkg/patchwork/R/patchwork.plot.r	2013-01-21 12:12:34 UTC (rev 156)
@@ -2,6 +2,11 @@
 							Reference=NULL,Alpha=0.0001,SD=1)
 	{
 
+	if(is.null(Normal.bam) & is.null(Reference))
+		{
+		stop("You must give either a normal bam or a reference file for patchwork to run properly! \n")
+		}
+
 	#Extract the name from tumor.bam
 
 	name = strsplit(tolower(Tumor.bam),".bam")
@@ -31,8 +36,8 @@
 			#If Normal.pileup exists, use with normal.vcf (if mpileup) or without (if pileup) to 
 			#create normalalf in patchwork.alleledata()
 
-			#Note that right not normalalf isnt even enabled.
-			#if (!is.null(Normal.pileup)) normalalf <- patchwork.alleledata(Normal.pileup, vcf=Normal.vcf)
+			#Create normalalf
+			if (!is.null(Normal.pileup)) normalalf <- patchwork.alleledata(Normal.pileup, vcf=Normal.vcf)
 
 			alf = patchwork.alleledata(Tumor.pileup, 
 												#normalalf=normalalf,

Modified: www/pw_exec.php
===================================================================
--- www/pw_exec.php	2013-01-04 10:48:00 UTC (rev 155)
+++ www/pw_exec.php	2013-01-21 12:12:34 UTC (rev 156)
@@ -328,7 +328,7 @@
 An example run of patchwork.copynumbers(): <br />
 
 <pre>
-	patchwork.copynumbers(CNFile="path/to/prefix_copynumbers.Rdata",cn2=0.8, delta=0.28, het=0.21, hom=0.79)
+	patchwork.copynumbers(CNfile="path/to/prefix_copynumbers.Rdata",cn2=0.8, delta=0.28, het=0.21, hom=0.79)
 </pre>
 
 This will generate an additional set of plots in your working directory. <br /><br />