[Patchwork-commits] r108 - pkg/patchwork/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Mar 12 17:05:58 CET 2012
Author: sebastian_d
Date: 2012-03-12 17:05:58 +0100 (Mon, 12 Mar 2012)
New Revision: 108
Modified:
pkg/patchwork/man/karyotype.Rd
pkg/patchwork/man/karyotype_check.Rd
pkg/patchwork/man/karyotype_chroms.Rd
pkg/patchwork/man/karyotype_chromsCN.Rd
pkg/patchwork/man/patchwork.GCNorm.Rd
pkg/patchwork/man/patchwork.Medians_n_AI.Rd
pkg/patchwork/man/patchwork.alleledata.Rd
pkg/patchwork/man/patchwork.applyref.Rd
pkg/patchwork/man/patchwork.createreference.Rd
pkg/patchwork/man/patchwork.readChroms.Rd
pkg/patchwork/man/patchwork.segment.Rd
pkg/patchwork/man/patchwork.smoothing.Rd
Log:
adding updated manual with new function names
Modified: pkg/patchwork/man/karyotype.Rd
===================================================================
--- pkg/patchwork/man/karyotype.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/karyotype.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -32,7 +32,7 @@
Allelic imbalance.
}
\item{name}{
- Default is the name of the input BamFile from patchwork.CNA().
+ Default is the name of the input BamFile from patchwork.plot().
Plot generated as "name.karyotype.png" in your working directory.
}
\item{xlim}{
@@ -44,8 +44,8 @@
}
\details{
-Vertical axis: Allelic imbalance. \cr
-Horizontal axis: Total intensity. \cr
+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().
}
@@ -73,7 +73,7 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}} \cr
+\code{\link{patchwork.plot}} \cr
\code{\link{karyotype_chroms}}
}
@@ -81,7 +81,7 @@
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/karyotype_check.Rd
===================================================================
--- pkg/patchwork/man/karyotype_check.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/karyotype_check.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -10,7 +10,7 @@
\description{
Plots the whole genome coverage vs allelic imbalance with the approximated
areas copynumbers and allele constitution. Karyotype_check is called from
-patchwork.findCNs function.
+patchwork.copynumbers function.
}
\usage{
@@ -43,7 +43,7 @@
A list between int and ai.
}
\item{name}{
- Default is BamFile argument from patchwork.CNA is used as argument.
+ Default is BamFile argument from patchwork.plot is used as argument.
}
\item{xlim}{
Default is c(-1.02,1.02). Limit of x axis.
@@ -69,7 +69,7 @@
The total number of alleles present are always the copynumber.
-Run within patchwork.findCNs function. findCNs.Rdata must be in working directory for that function
+Run within patchwork.copynumbers function. copynumbers.Rdata must be in working directory for that function
to run, and thus this one aswell as most of its input is taken from segs.
}
@@ -96,14 +96,14 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.findCNs}}
+\code{\link{patchwork.copynumbers}}
}
%\examples{
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/karyotype_chroms.Rd
===================================================================
--- pkg/patchwork/man/karyotype_chroms.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/karyotype_chroms.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -7,7 +7,7 @@
}
\description{
-Visualises the calculated data of patchwork.CNA() for each chromosome.
+Visualises the calculated data of patchwork.plot() for each chromosome.
See details for a walkthrough of the plot.
}
@@ -50,7 +50,7 @@
Inverse ratio between allele maximum and allele minimum.
}
\item{name}{
- Name of sample. patchwork.CNA sends it as name of the bamfile.
+ Name of sample. patchwork.plot sends it as name of the bamfile.
}
\item{xlim}{
Default is c(0,2.4). Limit of x axis.
@@ -109,7 +109,7 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}} \cr
+\code{\link{patchwork.plot}} \cr
\code{\link{karyotype}}
}
@@ -117,7 +117,7 @@
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/karyotype_chromsCN.Rd
===================================================================
--- pkg/patchwork/man/karyotype_chromsCN.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/karyotype_chromsCN.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -4,11 +4,11 @@
\title{
-Karyotype plotting for each chromosome post patchwork.findCNs().
+Karyotype plotting for each chromosome post patchwork.copynumbers().
}
\description{
-Visualises the calculated data of patchwork.CNA() + patchwork.findCns() for each chromosome.
+Visualises the calculated data of patchwork.plot() + patchwork.copynumbers() for each chromosome.
See details for a walkthrough of the plot.
}
@@ -57,7 +57,7 @@
Inverse ratio between allele maximum and allele minimum.
}
\item{name}{
- Name of sample. patchwork.CNA sends it as name of the bamfile.
+ Name of sample. patchwork.plot sends it as name of the bamfile.
}
\item{xlim}{
Default is c(-1.02,1.82). Limit of x axis.
@@ -125,14 +125,14 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.findCNs}}
+\code{\link{patchwork.copynumbers}}
}
%\examples{
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/patchwork.GCNorm.Rd
===================================================================
--- pkg/patchwork/man/patchwork.GCNorm.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/patchwork.GCNorm.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -48,14 +48,14 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
+\code{\link{patchwork.plot}}
}
%\examples{
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/patchwork.Medians_n_AI.Rd
===================================================================
--- pkg/patchwork/man/patchwork.Medians_n_AI.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/patchwork.Medians_n_AI.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -54,14 +54,14 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
+\code{\link{patchwork.plot}}
}
%\examples{
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/patchwork.alleledata.Rd
===================================================================
--- pkg/patchwork/man/patchwork.alleledata.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/patchwork.alleledata.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -19,14 +19,14 @@
\arguments{
\item{Pileup}{
- Pileup file from patchwork.CNA() input.
+ Pileup file from patchwork.plot() input.
}
}
\details{
Uses SNP data to calculate allele frequencies of the sample. Currently uses SNP132.
-patchwork.alleledata is a subfunction to patchwork.CNA.
+patchwork.alleledata is a subfunction to patchwork.plot.
}
%\value{
@@ -52,14 +52,14 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
+\code{\link{patchwork.plot}}
}
%\examples{
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/patchwork.applyref.Rd
===================================================================
--- pkg/patchwork/man/patchwork.applyref.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/patchwork.applyref.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -53,7 +53,7 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}} \cr
+\code{\link{patchwork.plot}} \cr
\code{\link{patchwork.createreference}}
}
@@ -61,7 +61,7 @@
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/patchwork.createreference.Rd
===================================================================
--- pkg/patchwork/man/patchwork.createreference.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/patchwork.createreference.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -8,7 +8,7 @@
}
\description{
-Create your own normal reference file for use with patchwork.CNA(). This may have advantages over using the
+Create your own normal reference file for use with patchwork.plot(). This may have advantages over using the
standard issue references. It is recommended to use atleast 3 bamfiles to create a
reference file.
}
@@ -34,9 +34,9 @@
specify, normalize them according to patchwork.readChroms and
patchwork.GCNorm. REFOUT.Rdata, or whichever name you chose, is created in your
working directory for further use. This file should then
-be sent in patchwork.CNA to be used as a reference file.
+be sent in patchwork.plot to be used as a reference file.
-patchwork.CNA(bamfile,pileup,reference="path/to/your/REFOUT.RData")
+patchwork.plot(bamfile,pileup,reference="path/to/your/REFOUT.Rdata")
}
%\value{
@@ -63,7 +63,7 @@
%\code{\link{help}}
\seealso{
-\code{\link{patchwork.CNA}} \cr
+\code{\link{patchwork.plot}} \cr
\code{\link{patchwork.readChroms}} \cr
\code{\link{patchwork.applyref}} \cr
\code{\link{patchwork.GCNorm}}
@@ -73,7 +73,7 @@
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/patchwork.readChroms.Rd
===================================================================
--- pkg/patchwork/man/patchwork.readChroms.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/patchwork.readChroms.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -8,7 +8,7 @@
}
\description{
-Internal function of patchwork.CNA().
+Internal function of patchwork.plot().
}
\usage{
@@ -17,7 +17,7 @@
\arguments{
\item{BamFile}{
- Input Bam from patchwork.CNA().
+ Input Bam from patchwork.plot().
}
\item{chroms}{
chroms is an object generated from pile.alleles.RData's alf\$achr attribute.
@@ -52,14 +52,14 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
+\code{\link{patchwork.plot}}
}
%\examples{
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/patchwork.segment.Rd
===================================================================
--- pkg/patchwork/man/patchwork.segment.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/patchwork.segment.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -6,7 +6,7 @@
}
\description{
-Internal function of patchwork.CNA().
+Internal function of patchwork.plot().
}
\usage{
@@ -21,12 +21,12 @@
chroms is an object generated from pile.alleles.RData's alf\$achr attribute.
}
\item{Alpha}{
- Default is inherited from patchwork.CNA() and is 0.0001.
+ Default is inherited from patchwork.plot() and is 0.0001.
From DNAcopy (?segment):
alpha: significance levels for the test to accept change-points.
}
\item{SD}{
- Default is inherited from patchwork.CNA() and is 1.
+ Default is inherited from patchwork.plot() and is 1.
From DNAcopy (?segment):
undo.SD: the number of SDs between means to keep a split if undo.splits="sdundo".
}
@@ -60,7 +60,7 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}} \cr
+\code{\link{patchwork.plot}} \cr
\code{\link{DNAcopy}} \cr
\code{\link{segment}}
}
@@ -69,7 +69,7 @@
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
Modified: pkg/patchwork/man/patchwork.smoothing.Rd
===================================================================
--- pkg/patchwork/man/patchwork.smoothing.Rd 2012-03-01 09:27:16 UTC (rev 107)
+++ pkg/patchwork/man/patchwork.smoothing.Rd 2012-03-12 16:05:58 UTC (rev 108)
@@ -51,14 +51,14 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
+\code{\link{patchwork.plot}}
}
%\examples{
%##---- Should be DIRECTLY executable !! ----
%##-- ==> Define data, use random,
%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
%}
% Add one or more standard keywords, see file 'KEYWORDS' in the
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