* collab:
update Rds
revert imputeGender to original api
bug fix for calculateRBafCNSet
update calculateRBafCNSet
Fix documentation for crlmmCopynumber -- added argument fitLinearModel
update crlmmGT2
Put rm(DD, ...) further down in crlmmGT2 function
remove message about cloning A and B
Open and close callsPr and callsGt in crlmmGT2 (when args not missing)
revert removed indices loaded in crlmmGT2
snprmaAffy no longer writes normalized intensities to calls and callProbability slots. crlmmGT2 takes arguments callsGt and callsPr. When present, crlmmGT2 will not overwrite A and B.
explicit coercion to matrix in imputeGender
Assign imputed gender to cnSet$gender within crlmmGT2 function.
Change sum(SNR > SNRmin) to sum(SNR[] > SNRmin) in imputeGender
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@69450 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 14/09/2012 20:07:37
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+\name{genotypeAffy}
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+\alias{genotypeAffy}
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+\title{Genotype Affymetrix CEL files}
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+\description{Assign diallelic genotypes at polymorphic markers}
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+\usage{
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+genotypeAffy(cnSet, SNRMin = 5, recallMin = 10, recallRegMin = 1000, gender = NULL, badSNP = 0.7, returnParams = TRUE, verbose = TRUE) |
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+} |
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+ |
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+\arguments{
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+ \item{cnSet}{
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+ An object of class \code{CNSet}
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+ } |
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+ \item{SNRMin}{
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+ See \code{\link{crlmm}}
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+ } |
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+ \item{recallMin}{
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+ See \code{\link{crlmm}}
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+} |
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+ \item{recallRegMin}{
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+ See \code{\link{crlmm}}
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+} |
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+ \item{gender}{
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+ See \code{\link{crlmm}}
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+} |
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+ \item{badSNP}{
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+ See \code{\link{crlmm}}
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+} |
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+ \item{returnParams}{
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+ See \code{\link{crlmm}}
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+} |
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+ \item{verbose}{
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+ Logical. |
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+} |
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+} |
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+\details{
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+ Wrapper for crlmm genotyping. |
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+} |
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+\value{
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+ Returns logical. SNP genotypes and confidence scores are written to |
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+ \code{ff_matrix} objects.
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+} |
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+ |
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+\author{
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+R.Scharpf |
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+} |
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+\seealso{
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+ \code{\link{crlmm}}, \code{\link{calls}}, \code{\link{confs}}
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+} |
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+\keyword{classif}
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\ No newline at end of file |