git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38548 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -109,3 +109,9 @@ is decoded and scanned |
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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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+* 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} |