[Patchwork-commits] r138 - pkg/patchwork/man

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

Author: sebastian_d
Date: 2012-06-25 16:01:50 +0200 (Mon, 25 Jun 2012)
New Revision: 138

Modified:
   pkg/patchwork/man/patchwork.copynumbers.Rd
   pkg/patchwork/man/subfunctions_copynumbers.Rd
Log:
some small updates to documentation for passing R CMD CHECK

Modified: pkg/patchwork/man/patchwork.copynumbers.Rd
===================================================================
--- pkg/patchwork/man/patchwork.copynumbers.Rd	2012-06-25 13:04:38 UTC (rev 137)
+++ pkg/patchwork/man/patchwork.copynumbers.Rd	2012-06-25 14:01:50 UTC (rev 138)
@@ -16,7 +16,7 @@
 }
 
 \usage{
-patchwork.copynumbers(CNfile,cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F)
+patchwork.copynumbers(CNfile,cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F,male.sample=F,male2femref=F)
 }
 
 \arguments{
@@ -42,9 +42,15 @@
   \item{ceiling}{
 	Default is 1.
 	}
-	\item{forcedelta}{
+  \item{forcedelta}{
 	Default is FALSE. If TRUE the delta value will not be subject to small adjustment changes.
 	}
+  \item{male.sample}{
+	Default is FALSE. If it is a male sample put TRUE here and it will handle the XY chromosomes better.
+	}
+  \item{male2femref}{
+	Default is FALSE. If TRUE the sample is male but the reference you used is female. This will correct for this.
+	}
 }
 
 \details{

Modified: pkg/patchwork/man/subfunctions_copynumbers.Rd
===================================================================
--- pkg/patchwork/man/subfunctions_copynumbers.Rd	2012-06-25 13:04:38 UTC (rev 137)
+++ pkg/patchwork/man/subfunctions_copynumbers.Rd	2012-06-25 14:01:50 UTC (rev 138)
@@ -6,6 +6,7 @@
 \alias{is.autosome}
 \alias{deChrom_ucsc}
 \alias{chrom_ucsc}
+\alias{assignAI}
 
 \title{
 A number of subfunctions used within patchwork.copynumbers().
@@ -29,6 +30,7 @@
 is.autosome(vector)
 deChrom_ucsc(data)
 chrom_ucsc(data)
+assignAI(snp_chr,snp_pos,snp_min,snp_max,seg_chr,seg_start,seg_end)
 }
 
 \arguments{
@@ -41,6 +43,27 @@
   \item{vector}{
 	The segs objects chr column.
 	}
+\item{snp_chr}{
+	Chromosome.
+	}
+\item{snp_pos}{
+	Position.
+	}
+\item{snp_min}{
+	Lesser allele amount in single position.
+	}
+\item{snp_max}{
+	Greater allele amount in single position.
+	}
+\item{seg_chr}{
+	Segments chromosome.
+	}
+\item{seg_start}{
+	Start position of segment.
+	}
+\item{seg_end}{
+	End position of segment.
+	}
 }
 
 %\details{