[Patchwork-commits] r111 - in pkg: patchwork/man patchworkCG/R patchworkCG/man patchworkData

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

Author: sebastian_d
Date: 2012-03-13 10:08:39 +0100 (Tue, 13 Mar 2012)
New Revision: 111

Modified:
   pkg/patchwork/man/patchwork.copynumbers.Rd
   pkg/patchworkCG/R/patchwork.CG.copynumbers.r
   pkg/patchworkCG/man/patchwork.CG.copynumbers.Rd
   pkg/patchworkCG/man/patchwork.CG.plot.Rd
   pkg/patchworkData/DESCRIPTION
Log:
Completed changes and updated documentation post functional namechanges

Modified: pkg/patchwork/man/patchwork.copynumbers.Rd
===================================================================
--- pkg/patchwork/man/patchwork.copynumbers.Rd	2012-03-12 16:29:00 UTC (rev 110)
+++ pkg/patchwork/man/patchwork.copynumbers.Rd	2012-03-13 09:08:39 UTC (rev 111)
@@ -45,7 +45,7 @@
 	Default is 1.
 	}
 	\item{forcedelta}{
-	Default is False.
+	Default is FALSE. If TRUE the delta value will not be subject to small adjustment changes.
 	}
 }
 

Modified: pkg/patchworkCG/R/patchwork.CG.copynumbers.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.copynumbers.r	2012-03-12 16:29:00 UTC (rev 110)
+++ pkg/patchworkCG/R/patchwork.CG.copynumbers.r	2012-03-13 09:08:39 UTC (rev 111)
@@ -1,4 +1,4 @@
-patchwork.CG.copynumbers = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV",CGfile=NULL,forcedelta=F)
+patchwork.CG.copynumbers = function(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_",CGfile=NULL,forcedelta=F)
 	{
 	data(ideogram,package="patchworkCG")
 	
@@ -275,7 +275,7 @@
     regions$mCn <- mCn
     regions$fullCN <- fullCN
     
-    save(regions,int,ai,file="CGCNV.Rdata")
+    save(regions,int,ai,file="copynumbers.Rdata")
     
 	write.csv(regions,file='Copynumbers.csv')
 	

Modified: pkg/patchworkCG/man/patchwork.CG.copynumbers.Rd
===================================================================
--- pkg/patchworkCG/man/patchwork.CG.copynumbers.Rd	2012-03-12 16:29:00 UTC (rev 110)
+++ pkg/patchworkCG/man/patchwork.CG.copynumbers.Rd	2012-03-13 09:08:39 UTC (rev 111)
@@ -20,7 +20,7 @@
 
 \usage{
 patchwork.CG.copynumbers(cn2,delta,het,hom,maxCn=8,ceiling=1,name="copynumbers_",
-				CGfile=NULL)
+				CGfile=NULL,forcedelta=F)
 }
 
 \arguments{
@@ -52,6 +52,9 @@
 	it to your working directory, you can simply input the path here as CGfile = "path/to/file/CG.Rdata"
 	so patchwork.CG.copynumbers() can find its data.
 	}
+	\item{forcedelta}{
+	Default is FALSE. If TRUE the delta value will be absolute and not subject to adjustments.
+	}
 }
 
 \details{

Modified: pkg/patchworkCG/man/patchwork.CG.plot.Rd
===================================================================
--- pkg/patchworkCG/man/patchwork.CG.plot.Rd	2012-03-12 16:29:00 UTC (rev 110)
+++ pkg/patchworkCG/man/patchwork.CG.plot.Rd	2012-03-13 09:08:39 UTC (rev 111)
@@ -1,6 +1,7 @@
 \name{patchwork.CG.plot}
 \alias{patchworkCG}
 \alias{patchwork.CG.plot}
+\alias{patchwork.CG}
 
 
 \title{
@@ -14,7 +15,7 @@
 }
 
 \usage{
-patchwork.CG(path,name='CG_sample_',manual_file_input=FALSE,
+patchwork.CG.plot(path=NULL,name='CG_sample',manual_file_input=FALSE,
 			masterVarBeta=NULL,somaticCnvSegments=NULL,
 			depthOfCoverage=NULL)
 }

Modified: pkg/patchworkData/DESCRIPTION
===================================================================
--- pkg/patchworkData/DESCRIPTION	2012-03-12 16:29:00 UTC (rev 110)
+++ pkg/patchworkData/DESCRIPTION	2012-03-13 09:08:39 UTC (rev 111)
@@ -10,3 +10,4 @@
 #LazyLoad: no
 #LazyData: yes
 Namespace: auto
+Depends: R (>= 2.10)
\ No newline at end of file