Browse code

Added documentation for SNPRMA

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38548 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/04/2009 11:22:53
Showing 4 changed files

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 2009-04-07 Rob Scharpf - committed version 1.0.73
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 * added cdfName as argument to computeCopynumber
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+2009-04-07 B Carvalho - committed versioni 1.0.74
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+
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+* Added documentation for snprma.
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+* Removed 'svn:executable' property of readIdatFiles.Rd
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays.
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-Version: 1.0.73
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+Version: 1.0.74
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 Date: 2008-12-30
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 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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+\name{snprma}
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+\Rdversion{1.1}
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+\alias{snprma}
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+
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+\title{
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+  Preprocessing tool for SNP arrays.
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+}
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+\description{
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+  SNPRMA will preprocess SNP chips. The preprocessing consists of
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+  quantile normalization to a known target distribution and
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+  summarization to the SNP-Allele level.
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+}
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+\usage{
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+snprma(filenames, mixtureSampleSize = 10^5, fitMixture = FALSE, eps = 0.1, verbose = TRUE, seed = 1, cdfName, sns)
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+}
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+\arguments{
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+  \item{filenames}{
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+    'character' vector with file names.
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+}
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+  \item{mixtureSampleSize}{
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+    Sample size to be use when fitting the mixture model.
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+}
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+  \item{fitMixture}{
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+    'logical'. Fit the mixture model?
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+}
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+  \item{eps}{
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+    Stop criteria.
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+}
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+  \item{verbose}{
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+    'logical'.
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+}
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+  \item{seed}{
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+    Seed to be used when sampling.
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+}
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+  \item{cdfName}{
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+    cdfName: 'GenomeWideSnp_5', 'GenomeWideSnp_6'
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+}
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+  \item{sns}{
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+    Sample names.
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+}
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+}
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+\value{
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+  \item{A}{Summarized intensities for Allele A}
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+  \item{B}{Summarized intensities for Allele B}
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+  \item{sns}{Sample names}
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+  \item{gns}{SNP names}
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+  \item{SNR}{Signal-to-noise ratio}
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+  \item{SKW}{Skewness}
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+  \item{mixtureParams}{Parameters from mixture model}
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+  \item{cdfName}{Name of the CDF}
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+}
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+\examples{
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+if (require(genomewidesnp5Crlmm) & require(hapmapsnp5)){
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+  path <- system.file("celFiles", package="hapmapsnp5")
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+
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+  ## the filenames with full path...
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+  ## very useful when genotyping samples not in the working directory
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+  cels <- list.celfiles(path, full.names=TRUE)
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+  snprmaOutput <- snprma(cels)
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+  snprmaOutput[["A"]][1:10,]
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+  snprmaOutput[["B"]][1:10,]
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+}
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+}
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+\keyword{manip}
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+\keyword{classif}