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\name{summarizeVariants}
\alias{summarizeVariants}
\alias{summarizeVariants,TxDb,VCF,CodingVariants-method}
\alias{summarizeVariants,TxDb,VCF,FiveUTRVariants-method}
\alias{summarizeVariants,TxDb,VCF,ThreeUTRVariants-method}
\alias{summarizeVariants,TxDb,VCF,SpliceSiteVariants-method}
\alias{summarizeVariants,TxDb,VCF,IntronVariants-method}
\alias{summarizeVariants,TxDb,VCF,PromoterVariants-method}
\alias{summarizeVariants,GRangesList,VCF,VariantType-method}
\alias{summarizeVariants,GRangesList,VCF,function-method}
\title{Summarize variants by sample}
\description{
Variants in a VCF file are overlapped with an annotation
region and summarized by sample. Genotype information in
the VCF is used to determine which samples express
each variant.
}
\usage{
\S4method{summarizeVariants}{TxDb,VCF,CodingVariants}(query, subject, mode, ...)
\S4method{summarizeVariants}{TxDb,VCF,FiveUTRVariants}(query, subject, mode, ...)
\S4method{summarizeVariants}{TxDb,VCF,ThreeUTRVariants}(query, subject, mode, ...)
\S4method{summarizeVariants}{TxDb,VCF,SpliceSiteVariants}(query, subject, mode, ...)
\S4method{summarizeVariants}{TxDb,VCF,IntronVariants}(query, subject, mode, ...)
\S4method{summarizeVariants}{TxDb,VCF,PromoterVariants}(query, subject, mode, ...)
\S4method{summarizeVariants}{GRangesList,VCF,VariantType}(query, subject, mode, ...)
\S4method{summarizeVariants}{GRangesList,VCF,function}(query, subject, mode, ...)
}
\arguments{
\item{query}{A \link[GenomicFeatures]{TxDb} or \code{GRangesList}
object that serves as the annotation. GFF files can be converted to
\link[GenomicFeatures]{TxDb} objects with
\code{makeTxDbFromGFF()} in the \code{GenomicFeatures} package.
}
\item{subject}{A \linkS4class{VCF} object containing the variants.
}
\item{mode}{\code{mode} can be a \code{VariantType} class or the
name of a function.
When \code{mode} is a \code{VariantType} class, counting is done with
\code{locateVariants} and counts are summarized transcript-by-sample.
Supported \code{VariantType} classes include
\code{CodingVariants}, \code{IntronVariants}, \code{FiveUTRVariants},
\code{ThreeUTRVariants}, \code{SpliceSiteVariants} or \code{PromoterVariants}.
\code{AllVariants()} and \code{IntergenicVariants} are not supported. See
?\code{locateVariants} for more detail on the variant classes.
\code{mode} can also be the name of any counting function that outputs
a \code{Hits} object. Variants will be summarized by the length of the
\code{GRangesList} annotation (i.e., 'length-of-GRangesList'-by-sample).
}
\item{\dots}{Additional arguments passed to methods such as
\describe{
\item{ignore.strand}{A \code{logical} indicating if strand should be
igored when performing overlaps.
}
}
}
}
\details{
\code{summarizeVariants} uses the genotype information in a VCF
file to determine which samples are positive for each variant.
Variants are overlapped with the annotation and the counts
are summarized annotation-by-sample. If the annotation is a
\code{GRangesList} of transcripts, the count matrix will
be transcripts-by-sample. If the \code{GRangesList} is genes,
the count matrix will be gene-by-sample.
\itemize{
\item{Counting with locateVariants() :}{
Variant counts are always summarized transcript-by-sample.
When \code{query} is a \code{GRangesList}, it must be compatible
with the \code{VariantType}-class given as the \code{mode} argument.
The list below specifies the appropriate \code{GRangesList} for each
\code{mode}.
\describe{
\item{CodingVariants :}{coding (CDS) by transcript}
\item{IntronVariants :}{introns by transcript}
\item{FiveUTRVariants :}{five prime UTR by transcript}
\item{ThreeUTRVariants :}{three prime UTR by transcript}
\item{SpliceSiteVariants :}{introns by transcript}
\item{PromoterVariants :}{list of transcripts}
}
When \code{query} is a \code{TxDb}, the appropriate
region-by-transcript \code{GRangesList} listed above is extracted
internally and used as the annotation.
}
\item{Counting with a user-supplied function :}{
\code{subject} must be a \code{GRangesList} and \code{mode} must
be the name of a function. The count function must take 'query'
and 'subject' arguments and return a \code{Hits} object. Counts are
summarized by the outer list elements of the \code{GRangesList}.
}
}
}
\value{
A \code{RangedSummarizedExperiment} object with count summaries in the
\code{assays} slot. The \code{rowRanges} contains the annotation
used for counting. Information in \code{colData} and \code{metadata}
are taken from the VCF file.
}
\author{Valerie Obenchain}
\seealso{
\code{\link{readVcf}},
\code{\link{predictCoding}},
\code{\link{locateVariants}}
}
\examples{
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
## Read variants from VCF.
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
## Rename seqlevels to match TxDb; confirm the match.
seqlevels(vcf) <- paste0("chr", seqlevels(vcf))
intersect(seqlevels(vcf), seqlevels(txdb))
## ----------------------------------------
## Counting with locateVariants()
## ----------------------------------------
## TxDb as the 'query'
coding1 <- summarizeVariants(txdb, vcf, CodingVariants())
colSums(assays(coding1)$counts)
## GRangesList as the 'query'
cdsbytx <- cdsBy(txdb, "tx")
coding2 <- summarizeVariants(cdsbytx, vcf, CodingVariants())
stopifnot(identical(assays(coding1)$counts, assays(coding2)$counts))
## Promoter region variants summarized by transcript
tx <- transcripts(txdb)
txlst <- splitAsList(tx, seq_len(length(tx)))
promoter <- summarizeVariants(txlst, vcf,
PromoterVariants(upstream=100, downstream=10))
colSums(assays(promoter)$counts)
## ----------------------------------------
## Counting with findOverlaps()
## ----------------------------------------
## Summarize all variants by transcript
allvariants <- summarizeVariants(txlst, vcf, findOverlaps)
colSums(assays(allvariants)$counts)
}
\keyword{methods}
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