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\name{GLtoGP}
\alias{GLtoGP}
\title{Convert genotype likelihoods to genotype probabilities}
\description{
Convert an array of genotype likelihoods to
posterior genotype probabilities.
}
\usage{
GLtoGP(gl)
}
\arguments{
\item{gl}{Array of genotype likelihoods. The format can be a matrix
of lists, or a three-dimensional array in which the third dimension
corresponds to the probabilities for each genotype.}
}
\details{
Computes the probability of each genotype as \code{10^x / sum(10^x)}.
}
\value{
An array of posterior genotype probabilities, in the same format as
the input (matrix of lists or 3D array).
}
\author{
Stephanie Gogarten <sdmorris@u.washington.edu>
}
\seealso{
\link{readVcf},
\link{genotypeToSnpMatrix}
}
\examples{
## Read a vcf file with a "GL" field.
vcfFile <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation")
vcf <- readVcf(vcfFile, "hg19")
## extract genotype likelihoods as a matrix of lists
gl <- geno(vcf)$GL
class(gl)
mode(gl)
# convert to posterior probabilities
gp <- GLtoGP(gl)
}
\keyword{manip}
|
