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\name{genotypeToSnpMatrix}
\alias{genotypeToSnpMatrix}
\alias{genotypeToSnpMatrix,CollapsedVCF-method}
\alias{genotypeToSnpMatrix,array-method}
\title{Convert genotype calls from a VCF file to a SnpMatrix object}
\description{
Convert an array of genotype calls from the "GT", "GP", or "GL"
FORMAT field of a VCF file to a \link[snpStats:SnpMatrix-class]{SnpMatrix}.
}
\usage{
\S4method{genotypeToSnpMatrix}{CollapsedVCF}(x, uncertain=FALSE, ...)
\S4method{genotypeToSnpMatrix}{array}(x, ref, alt, ...)
}
\arguments{
\item{x}{
A \code{CollapsedVCF} object or a \code{array} of genotype data
from the "GT", "GP", or "GL" FORMAT field of a VCF file. This \code{array} is created
with a call to \code{readVcf} and can be accessed with \code{geno(<VCF>)}.
}
\item{uncertain}{
A logical indicating whether the genotypes to convert
should come from the "GT" field (\code{uncertain=FALSE}) or the "GP" or
"GL" field (\code{uncertain=TRUE}).
}
\item{ref}{
A \code{DNAStringSet} of reference alleles.
}
\item{alt}{
A \code{DNAStringSetList} of alternate alleles.
}
\item{\dots}{
Additional arguments, passed to methods.
}
}
\details{
\code{genotypeToSnpMatrix} converts an array of genotype calls from the
"GT", "GP", or "GL" FORMAT field of a VCF file into a
\link[snpStats:SnpMatrix-class]{SnpMatrix}. The following caveats apply,
\itemize{
\item{no distinction is made between phased and unphased genotypes}
\item{variants with >1 ALT allele are set to NA}
\item{only single nucleotide variants are included; others are set to NA}
\item{only diploid calls are included; others are set to NA}
}
In VCF files, 0 represents the reference allele and integers greater than 0
represent the alternate alleles (i.e., 2, 3, 4 would indicate the 2nd, 3rd
or 4th allele in the ALT field for a particular variant). This function only
supports variants with a single alternate allele and therefore the alternate
values will always be 1. Genotypes are stored in the SnpMatrix
as 0, 1, 2 or 3 where 0 = missing, 1 = "0/0", 2 = "0/1" or "1/0" and
3 = "1/1". In SnpMatrix terminology, "A" is the reference allele
and "B" is the risk allele. Equivalent statements to those made with 0 and 1
allele values would be 0 = missing, 1 = "A/A", 2 = "A/B" or "B/A" and
3 = "B/B".
The three genotype fields are defined as follows:
\itemize{
\item{GT : genotype, encoded as allele values separated by either of
"/" or "|". The allele values are 0 for the reference allele and 1
for the alternate allele.}
\item{GL : genotype likelihoods comprised of comma separated
floating point log10-scaled likelihoods for all possible
genotypes. In the case of a reference allele A and a single
alternate allele B, the likelihoods will be ordered "A/A", "A/B", "B/B".}
\item{GP : the phred-scaled genotype posterior probabilities for all
possible genotypes; intended to store
imputed genotype probabilities. The ordering of values is the
same as for the GL field.}
}
If \code{uncertain=TRUE}, the posterior probabilities of the three
genotypes ("A/A", "A/B", "B/B") are encoded (approximately) as byte
values. This encoding allows uncertain genotypes to be used in
\link[snpStats]{snpStats} functions, which in some cases may be more
appropriate than using only the called genotypes. The byte encoding
conserves memory by allowing the uncertain genotypes to be stored in a
two-dimensional raw matrix.
See the \link[snpStats]{snpStats} documentation for more details.
}
\value{
A list with the following elements,
\item{genotypes}{
The output genotype data as an object of class
\code{"SnpMatrix"}. The columns are snps and the rows are the samples.
See ?\code{SnpMatrix} details of the class structure.
}
\item{map}{
A \code{DataFrame} giving the snp names and alleles at each locus.
The \code{ignore} column indicates which variants were set to \code{NA}
(see \code{NA} criteria in 'details' section).
}
}
\references{
\url{http://www.1000genomes.org/wiki/Analysis/Variant\%20Call\%20Format/vcf-variant-call-format-version-41}
}
\author{
Stephanie Gogarten, Valerie Obenchain <vobencha@fhcrc.org>
}
\seealso{
\link{readVcf},
\linkS4class{VCF},
\link[snpStats:SnpMatrix-class]{SnpMatrix}
}
\examples{
## ----------------------------------------------------------------
## Non-probability based snp encoding using "GT"
## ----------------------------------------------------------------
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
## This file has no "GL" or "GP" field so we use "GT".
geno(vcf)
## Convert the "GT" FORMAT field to a SnpMatrix.
mat <- genotypeToSnpMatrix(vcf)
## The result is a list of length 2.
names(mat)
## Compare coding in the VCF file to the SnpMatrix.
geno(vcf)$GT
t(as(mat$genotype, "character"))
## The 'ignore' column in 'map' indicates which variants
## were set to NA. Variant rs6040355 was ignored because
## it has multiple alternate alleles, microsat1 is not a
## snp, and chr20:1230237 has no alternate allele.
mat$map
## ----------------------------------------------------------------
## Probability-based encoding using "GL" or "GP"
## ----------------------------------------------------------------
## Read a vcf file with a "GL" field.
fl <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
geno(vcf)
## Convert the "GL" FORMAT field to a SnpMatrix
mat <- genotypeToSnpMatrix(vcf, uncertain=TRUE)
## Only 3 of the 9 variants passed the filters. The
## other 6 variants had no alternate alleles.
mat$map
## Compare genotype representations for a subset of
## samples in variant rs180734498.
## Original called genotype
geno(vcf)$GT["rs180734498", 14:16]
## Original genotype likelihoods
geno(vcf)$GL["rs180734498", 14:16]
## Posterior probability (computed inside genotypeToSnpMatrix)
GLtoGP(geno(vcf)$GL["rs180734498", 14:16, drop=FALSE])[1,]
## SnpMatrix coding.
t(as(mat$genotype, "character"))["rs180734498", 14:16]
t(as(mat$genotype, "numeric"))["rs180734498", 14:16]
## For samples NA11829 and NA11830, one probability is significantly
## higher than the others, so SnpMatrix calls the genotype. These
## calls match the original coding: "0|1" -> "A/B", "0|0" -> "A/A".
## Sample NA11831 was originally called as "0|1" but the probability
## of "0|0" is only a factor of 3 lower, so SnpMatrix calls it as
## "Uncertain" with an appropriate byte-level encoding.
}
\keyword{manip}
\keyword{methods}
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