[Patchwork-commits] r32 - in pkg/patchwork: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Nov 29 12:05:00 CET 2011
Author: sebastian_d
Date: 2011-11-29 12:04:59 +0100 (Tue, 29 Nov 2011)
New Revision: 32
Modified:
pkg/patchwork/R/patchwork.findCNs.r
pkg/patchwork/man/karyotype.Rd
pkg/patchwork/man/karyotype_chroms.Rd
pkg/patchwork/man/karyotype_chromsCN.Rd
pkg/patchwork/man/patchwork.CNA.Rd
pkg/patchwork/man/patchwork.findCNs.Rd
pkg/patchwork/man/subfunctions_findCNs.Rd
Log:
More documentation and code updates.
Modified: pkg/patchwork/R/patchwork.findCNs.r
===================================================================
--- pkg/patchwork/R/patchwork.findCNs.r 2011-11-28 16:34:09 UTC (rev 31)
+++ pkg/patchwork/R/patchwork.findCNs.r 2011-11-29 11:04:59 UTC (rev 32)
@@ -1,4 +1,4 @@
-patchwork.findCNs = function(cn2=NULL,delta=NULL,het=NULL,hom=NULL,maxCn=8,ceiling=1)
+patchwork.findCNs = function(cn2,delta,het,hom,maxCn=8,ceiling=1)
{
packagepath = system.file(package="patchwork")
Modified: pkg/patchwork/man/karyotype.Rd
===================================================================
--- pkg/patchwork/man/karyotype.Rd 2011-11-28 16:34:09 UTC (rev 31)
+++ pkg/patchwork/man/karyotype.Rd 2011-11-29 11:04:59 UTC (rev 32)
@@ -12,7 +12,7 @@
}
\usage{
-karyotype(chr,start,end,int,ai,name,xlim,ylim)
+karyotype(chr,start,end,int,ai,chroms,name,xlim,ylim)
}
\arguments{
@@ -47,8 +47,8 @@
}
\details{
-Vertical axis: Allelic imbalance. \\
-Horizontal axis: Total intensity. \\
+Vertical axis: Allelic imbalance. \cr
+Horizontal axis: Total intensity. \cr
The plot is a overview, for a closer look see the plots generated by karyotype_chroms().
}
Modified: pkg/patchwork/man/karyotype_chroms.Rd
===================================================================
--- pkg/patchwork/man/karyotype_chroms.Rd 2011-11-28 16:34:09 UTC (rev 31)
+++ pkg/patchwork/man/karyotype_chroms.Rd 2011-11-29 11:04:59 UTC (rev 32)
@@ -66,9 +66,9 @@
\details{
Walkthrough of the plot:
-\textbf{TOP} \\
-Vertical axis: Allelic Imbalance \\
-Horizontal axis: Total Intensity \\
+\bold{TOP} \cr
+Vertical axis: Allelic Imbalance \cr
+Horizontal axis: Total Intensity \cr
The chromosome plotted against the complete genome background. The separation between
clusters within the plot are due to the fluctuating intensity and allelic imbalance
@@ -76,15 +76,15 @@
Longer/larger segments have bigger circles. Darker circles show more content as they are
ontop of eachother.
-\textbf{MIDDLE} \\
-Vertical axis: Total Intensity \\
-Horizontal axis: Chromosomal coordinate \\
+\bold{MIDDLE} \cr
+Vertical axis: Total Intensity \cr
+Horizontal axis: Chromosomal coordinate \cr
The chromosome in questions total intensity plotted against the position on the chromosome.
-\textbf{BOTTOM} \\
-Vertical axis: Allelic Imbalance \\
-Horizontal axis: Chromosomal coordinate \\
+\bold{BOTTOM} \cr
+Vertical axis: Allelic Imbalance \cr
+Horizontal axis: Chromosomal coordinate \cr
The chromosome in questions allelic imbalance plotted against the position on the chromosome.
}
Modified: pkg/patchwork/man/karyotype_chromsCN.Rd
===================================================================
--- pkg/patchwork/man/karyotype_chromsCN.Rd 2011-11-28 16:34:09 UTC (rev 31)
+++ pkg/patchwork/man/karyotype_chromsCN.Rd 2011-11-29 11:04:59 UTC (rev 32)
@@ -13,7 +13,7 @@
}
\usage{
-karyotype_chromsCN(chr,start,end,int,ai,chroms,mchr,mpos,mval,schr,spos,sval,name,xlim,ylim,maxCN=8)
+karyotype_chromsCN(chr,start,end,int,ai,Cn,mCn,mchr,mpos,mval,schr,spos,sval,name='',xlim=c(-1.02,1.82),ylim=0:1,maxCn=8)
}
\arguments{
@@ -32,9 +32,12 @@
\item{ai}{ %segs$ai
Allelic imbalance.
}
- \item{chroms}{
- Object created in patchwork.CNA which holds chromosome names.
+ \item{Cn}{
+ Copy number.
}
+ \item{mCn}{
+ mCn.
+ }
\item{mchr}{
Chromosomes name of kbsegs object. Final version of kbsegs created from patchwork.smoothing().
}
@@ -57,12 +60,12 @@
Name of sample. patchwork.CNA sends it as name of the bamfile.
}
\item{xlim}{
- Default is c(0,2.4). Limit of x axis.
+ Default is c(-1.02,1.82). Limit of x axis.
}
\item{ylim}{
- Default is c(0.3,1). Limit of y axis.
+ Default is 0:1. Limit of y axis.
}
- \item{maxCN}{
+ \item{maxCn}{
Default is 8. The highest copynumber of the sample to check for.
}
}
@@ -70,9 +73,9 @@
\details{
Walkthrough of the plot:
-\textbf{TOP} \\
-Vertical axis: Allelic Imbalance \\
-Horizontal axis: Total Intensity \\
+\bold{TOP} \cr
+Vertical axis: Allelic Imbalance \cr
+Horizontal axis: Total Intensity \cr
The chromosome plotted against the complete genome background. The separation between
clusters within the plot are due to the fluctuating intensity and allelic imbalance
@@ -80,21 +83,21 @@
Longer/larger segments have bigger circles. Darker circles show more content as they are
ontop of eachother.
-\textbf{TOP MIDDLE} \\
-Vertical axis: Copynumber \\
-Horizontal axis: Chromosomal coordinate \\
+\bold{TOP MIDDLE} \cr
+Vertical axis: Copynumber \cr
+Horizontal axis: Chromosomal coordinate \cr
Displays the total and minor copynumbers for different segments of the chromosome in question.
-\textbf{LOWER MIDDLE} \\
-Vertical axis: Total Intensity \\
-Horizontal axis: Chromosomal coordinate \\
+\bold{LOWER MIDDLE} \cr
+Vertical axis: Total Intensity \cr
+Horizontal axis: Chromosomal coordinate \cr
The chromosome in questions total intensity plotted against the position on the chromosome.
-\textbf{BOTTOM} \\
-Vertical axis: Allelic Imbalance \\
-Horizontal axis: Chromosomal coordinate \\
+\bold{BOTTOM} \cr
+Vertical axis: Allelic Imbalance \cr
+Horizontal axis: Chromosomal coordinate \cr
The chromosome in questions allelic imbalance plotted against the position on the chromosome.
}
@@ -121,9 +124,9 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
-%\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-%}
+\seealso{
+\code{\link{patchwork.findCNs}}
+}
%\examples{
%##---- Should be DIRECTLY executable !! ----
Modified: pkg/patchwork/man/patchwork.CNA.Rd
===================================================================
--- pkg/patchwork/man/patchwork.CNA.Rd 2011-11-28 16:34:09 UTC (rev 31)
+++ pkg/patchwork/man/patchwork.CNA.Rd 2011-11-29 11:04:59 UTC (rev 32)
@@ -45,7 +45,7 @@
}
\details{
-\textbf{Make sure to only run one sample at a time in a single working directory
+\bold{Make sure to only run one sample at a time in a single working directory
as standard file names are created. If you do not heed this warning you
will end up with a complete mess and probably runtime errors as patchwork.readChroms
tries to run simultaniously for multiple samples in the same working directory.}
Modified: pkg/patchwork/man/patchwork.findCNs.Rd
===================================================================
--- pkg/patchwork/man/patchwork.findCNs.Rd 2011-11-28 16:34:09 UTC (rev 31)
+++ pkg/patchwork/man/patchwork.findCNs.Rd 2011-11-29 11:04:59 UTC (rev 32)
@@ -1,41 +1,44 @@
\name{patchwork.findCNs}
+\alias{patchwork.findCNs}
\alias{findCNs}
-\alias{patchwork.findCNs}
+
\title{
-Function to find Copy Numbers
+Function plot allele-specific copy numbers of the genome
}
\description{
-Given input data from user regarding plots generated through patchwork.CNA
-this function will find copy numbers or something..
+Input data for this function should be assessed from any of the karyotype_chroms()
+plots. For example <yoursample>_karyotype.chr<1-22,X,Y>.png.
-Very important: For this function to work you must have the file findCNs.Rdata,
-generated using patchwork.CNA function, in your working directory!
+See argument details.
+
+\bold{Very important: For this function to work you must have the file findCNs.Rdata,
+generated using patchwork.CNA function, in your working directory!}
}
\usage{
-patchwork.findCNs(cn2=NULL,delta=NULL,het=NULL,hom=NULL,maxCn=8,ceiling=1))
+patchwork.findCNs(cn2,delta,het,hom,maxCn=8,ceiling=1)
}
\arguments{
\item{cn2}{
- description
+ The approximate position of copy number two on total intensity axis.
}
\item{delta}{
- description
+ The difference in total intensity between consecutive copy numbers. For example 1 and 2 or 2 and 3.
}
\item{het}{
- description
+ Allelic imbalance ratio of heterozygous copy number 2.
}
\item{hom}{
- description
+ Allelic imbalance ratio of Loss-of-heterozygosity copy number 2.
}
\item{maxCn}{
- description
+ Highest copy number to calculate for. Default is 8.
}
\item{ceiling}{
- description
+ Default is 1.
}
}
@@ -70,7 +73,7 @@
\seealso{
\code{\link{patchwork.CNA}}
-\code{\link{subfunctions_findCNss}}
+\code{\link{subfunctions_findCNs}}
}
%\examples{
Modified: pkg/patchwork/man/subfunctions_findCNs.Rd
===================================================================
--- pkg/patchwork/man/subfunctions_findCNs.Rd 2011-11-28 16:34:09 UTC (rev 31)
+++ pkg/patchwork/man/subfunctions_findCNs.Rd 2011-11-29 11:04:59 UTC (rev 32)
@@ -25,19 +25,19 @@
\arguments{
\item{data}{
- description
+ Object to be handled by the internal function.
}
\item{weights}{
- description
+ Weights to be applied.
}
\item{vector}{
The segs objects chr column.
}
}
-\details{
-Details
-}
+%\details{
+%Details
+%}
%\value{
%% ~Describe the value returned
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