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\name{VariantAnnotation-defunct}
\alias{VariantAnnotation-defunct}
\alias{refLocsToLocalLocs}
\alias{refLocsToLocalLocs,GRanges,TxDb,missing-method}
\alias{refLocsToLocalLocs,GRanges,missing,GRangesList-method}
\alias{readVcfLongForm}
\alias{readVcfLongForm,TabixFile,character,GRanges-method}
\alias{readVcfLongForm,TabixFile,character,missing-method}
\alias{readVcfLongForm,TabixFile,character,IntegerRangesList-method}
\alias{readVcfLongForm,TabixFile,character,ScanVcfParam-method}
\alias{readVcfLongForm,character,character,ScanVcfParam-method}
\alias{readVcfLongForm,character,character,missing-method}
\alias{readVcfLongForm,character,missing,missing-method}
\alias{dbSNPFilter}
\alias{regionFilter}
\alias{MatrixToSnpMatrix}
\alias{VRangesScanVcfParam}
\alias{restrictToSNV}
\title{Defunct Functions in Package \code{VariantAnnotation}}
\description{
The functions or variables listed here are no longer part
of \code{VariantAnnotation}.
}
\section{usage}{
## Removed
\itemize{
\item refLocsToLocalLocs()
\item readVcfLongForm()
\item dbSNPFilter()
\item regionFilter()
\item MatrixToSnpMatrix()
\item getTranscriptSeqs()
\item VRangesScanVcfParam()
\item restrictToSNV()
}
}
\details{
## Removed
\itemize{
\item{
\code{refLocsToLocalLocs} has been replaced by \code{mapToTranscripts}
and \code{pmapToTranscripts}.
}
\item{
\code{readVcfLongForm} has been replaced by \code{expand}.
}
\item{
\code{dbSNPFilter} and \code{regionFilter} have been replaced by
\code{filterVcf}.
}
\item{
\code{regionFilter} has been replaced by \code{filterVcf}.
}
\item{
\code{MatrixToSnpMatrix} has been replaced by \code{genotypeToSnpMatrix}.
}
\item{
\code{getTranscriptSeqs} has been replaced by
\code{extractTranscriptSeqs} in the GenomicFeatures package.
}
\item{
\code{VRangesScanVcfParam} has been replaced by \code{ScanVcfParam}.
}
\item{
\code{restrictToSVN} has been replaced by \code{isSNV}.
}
}
}
\author{
Valerie Obenchain
}
\seealso{
\itemize{
\item \code{\link{expand}}
\item \code{\link{filterVcf}}
\item \code{\link{genotypeToSnpMatrix}}
\item \code{\link[GenomicFeatures]{mapToTranscripts}}
\item \code{\link[GenomicFeatures]{extractTranscriptSeqs}}
\item \code{\link{isSNV}}
\item \code{\link{ScanVcfParam}}
}
}
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