[Patchwork-commits] r110 - pkg/patchwork/man

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

Author: sebastian_d
Date: 2012-03-12 17:29:00 +0100 (Mon, 12 Mar 2012)
New Revision: 110

Modified:
   pkg/patchwork/man/karyotype_chroms.Rd
   pkg/patchwork/man/patchwork.alleledata.Rd
   pkg/patchwork/man/patchwork.copynumbers.Rd
   pkg/patchwork/man/patchwork.plot.Rd
   pkg/patchwork/man/patchwork.segment.Rd
   pkg/patchwork/man/patchwork.smoothing.Rd
Log:
commit post fixing some codoc missmatches in patchwork

Modified: pkg/patchwork/man/karyotype_chroms.Rd
===================================================================
--- pkg/patchwork/man/karyotype_chroms.Rd	2012-03-12 16:10:08 UTC (rev 109)
+++ pkg/patchwork/man/karyotype_chroms.Rd	2012-03-12 16:29:00 UTC (rev 110)
@@ -1,6 +1,5 @@
 \name{karyotype_chroms}
 \alias{karyotype_chroms}
-\alias{patchwork.plot}
 
 \title{
 Karyotype plotting of each chromosome

Modified: pkg/patchwork/man/patchwork.alleledata.Rd
===================================================================
--- pkg/patchwork/man/patchwork.alleledata.Rd	2012-03-12 16:10:08 UTC (rev 109)
+++ pkg/patchwork/man/patchwork.alleledata.Rd	2012-03-12 16:29:00 UTC (rev 110)
@@ -14,14 +14,18 @@
 }
 
 \usage{
-patchwork.alleledata(Pileup)
+patchwork.alleledata(Pileup, normalalf=NULL)
 }
 
 \arguments{
   \item{Pileup}{
   	Pileup file from patchwork.plot() input.
 	}
+\item{normalalf}{
+	normalalf is generated and used if you have supplied a normal.pileup in its argument
+	at patchwork.plot.
 }
+}
 
 \details{
 Uses SNP data to calculate allele frequencies of the sample. Currently uses SNP132.

Modified: pkg/patchwork/man/patchwork.copynumbers.Rd
===================================================================
--- pkg/patchwork/man/patchwork.copynumbers.Rd	2012-03-12 16:10:08 UTC (rev 109)
+++ pkg/patchwork/man/patchwork.copynumbers.Rd	2012-03-12 16:29:00 UTC (rev 110)
@@ -18,7 +18,7 @@
 }
 
 \usage{
-patchwork.copynumbers(name="copynumbers_"cn2,delta,het,hom,maxCn=8,ceiling=1)
+patchwork.copynumbers(name="copynumbers_",cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F)
 }
 
 \arguments{
@@ -44,6 +44,9 @@
   \item{ceiling}{
 	Default is 1.
 	}
+	\item{forcedelta}{
+	Default is False.
+	}
 }
 
 \details{

Modified: pkg/patchwork/man/patchwork.plot.Rd
===================================================================
--- pkg/patchwork/man/patchwork.plot.Rd	2012-03-12 16:10:08 UTC (rev 109)
+++ pkg/patchwork/man/patchwork.plot.Rd	2012-03-12 16:29:00 UTC (rev 110)
@@ -19,7 +19,7 @@
 }
 
 \usage{
-patchwork.plot(BamFile,Pileup,reference=NULL,normal.bam=NULL,normal.pileup=NULLAlpha=0.0001,SD=1)
+patchwork.plot(BamFile,Pileup,reference=NULL,normal.bam=NULL,normal.pileup=NULL,Alpha=0.0001,SD=1)
 }
 
 \arguments{

Modified: pkg/patchwork/man/patchwork.segment.Rd
===================================================================
--- pkg/patchwork/man/patchwork.segment.Rd	2012-03-12 16:10:08 UTC (rev 109)
+++ pkg/patchwork/man/patchwork.segment.Rd	2012-03-12 16:29:00 UTC (rev 110)
@@ -34,7 +34,9 @@
 
 \details{
 Performs a segmentation using various functions of DNAcopy package and returns the segments
-in a new object called "segs", saved in Segments.Rdata.
+in a new object called "segs", saved in Segments.Rdata. \cr
+
+See ?DNAcopy
 }
 
 %\value{
@@ -61,8 +63,6 @@
 
 \seealso{
 \code{\link{patchwork.plot}} \cr
-\code{\link{DNAcopy}}	\cr
-\code{\link{segment}}
 }
 
 %\examples{

Modified: pkg/patchwork/man/patchwork.smoothing.Rd
===================================================================
--- pkg/patchwork/man/patchwork.smoothing.Rd	2012-03-12 16:10:08 UTC (rev 109)
+++ pkg/patchwork/man/patchwork.smoothing.Rd	2012-03-12 16:29:00 UTC (rev 110)
@@ -12,13 +12,19 @@
 }
 
 \usage{
-patchwork.smoothing(data,chroms)
+patchwork.smoothing(data,normaldata=NULL,reference=NULL,chroms)
 }
 
 \arguments{
   \item{data}{
   	data object generated after patchwork.GCNorm().
 	}
+	\item{normaldata}{
+	Default is NULL, generated and used if you have supplied normal.bam to patchwork.plot.
+	}
+	\item{reference}{
+	Default is NULL, used if you have supplied reference argument to patchwork.plot.
+	}
   \item{chroms}{
 	chroms is an object generated from pile.alleles.RData's alf\$achr attribute.
 	}