[Patchwork-commits] r87 - pkg/patchwork/R

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

Author: mayrhofer
Date: 2012-02-13 11:26:44 +0100 (Mon, 13 Feb 2012)
New Revision: 87

Modified:
   pkg/patchwork/R/patchwork.CNA.r
   pkg/patchwork/R/patchwork.applyref.r
Log:
debugs

Modified: pkg/patchwork/R/patchwork.CNA.r
===================================================================
--- pkg/patchwork/R/patchwork.CNA.r	2012-02-09 15:39:20 UTC (rev 86)
+++ pkg/patchwork/R/patchwork.CNA.r	2012-02-13 10:26:44 UTC (rev 87)
@@ -1,4 +1,4 @@
-patchwork.CNA <- function(BamFile,Pileup,reference,normal.bam=NULL,normal.pileup=NULL,Alpha=0.0001,SD=1)
+patchwork.CNA <- function(BamFile,Pileup,reference='illumina',normal.bam=NULL,normal.pileup=NULL,Alpha=0.0001,SD=1)
 	{
 	#library(patchwork)
 	#patchwork.CNA("cancer.bam","pile.up",reference="illumina")
@@ -64,6 +64,22 @@
 		try ( load('normaldata.Rdata'), silent=TRUE )
 		if(is.null(normaldata))
 			{
+			filename=strsplit(normal.bam,'/')[[1]]; filename=filename[length(filename)]
+			path=strsplit(normal.bam,paste('/',filename,sep=''))[[1]][1]
+			olddir=getwd(); setwd(path); path=getwd(); setwd(olddir)
+			if (path != getwd()) {
+				temp=data; data=NULL
+				try( load(paste(path,'data.Rdata',sep='/')), silent=T )
+				if (is.null(data)) {
+				data=temp
+				} else {
+					normaldata=data
+					data=temp
+				}
+			}
+		}
+		if(is.null(normaldata))
+			{
 			cat("Initiating Read Chroms (matched normal) \n")
 			normaldata = patchwork.readChroms(BamFile,chroms)
 			cat("Read Chroms Complete (matched normal) \n")
@@ -85,7 +101,9 @@
 	if(length(data) < 9)
 		{
 		cat("Initiating Application of Reference \n")
-		if (!is.null(normal.bam)) data <- patchwork.applyref(data,reference=reference) else data <- patchwork.applyref(data,normaldata=normaldata)
+		if (is.null(normal.bam)) {
+			data <- patchwork.applyref(data,reference=reference)
+		} else data <- patchwork.applyref(data,normaldata=normaldata)
 		cat("Application of Reference Complete \n")
 		save(data,file='data.Rdata')
 		}

Modified: pkg/patchwork/R/patchwork.applyref.r
===================================================================
--- pkg/patchwork/R/patchwork.applyref.r	2012-02-09 15:39:20 UTC (rev 86)
+++ pkg/patchwork/R/patchwork.applyref.r	2012-02-13 10:26:44 UTC (rev 87)
@@ -2,7 +2,12 @@
 	{
 
 	if (!is.null(reference)) load(reference)
-		
+	
+	if (!is.null(normaldata)) {
+		normaldata=normaldata[,c(1,2,7)]
+		colnames(normaldata)[3]='norm_mean'
+	}
+
 	data <- merge(data[,1:7],normaldata,all=F,by=1:2)
 	#data$ratio <- data$norm / data$norm_mean
 	data$reference <- data$norm_mean  ## thats temporary