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\name{snpSummary}
\alias{snpSummary}
\alias{snpSummary,CollapsedVCF-method}
\title{Counts and distribution statistics for SNPs in a VCF object}
\description{
Counts and distribution statistics for SNPs in a VCF object
}
\usage{
\S4method{snpSummary}{CollapsedVCF}(x, ...)
}
\arguments{
\item{x}{
A \link{CollapsedVCF} object.
}
\item{\dots}{
Additional arguments to methods.
}
}
\details{
Genotype counts, allele counts and Hardy Weinberg equilibrium
(HWE) statistics are calculated for single nucleotide variants
in a \link{CollapsedVCF} object. HWE has been established as a
useful quality filter on genotype data. This equilibrium should
be attained in a single generation of random mating. Departures
from HWE are indicated by small p values and are almost invariably
indicative of a problem with genotype calls.
The following caveats apply:
\itemize{
\item No distinction is made between phased and unphased genotypes.
\item Only diploid calls are included.
\item Only `valid' SNPs are included. A `valid' SNP is defined
as having a reference allele of length 1 and a single
alternate allele of length 1.
}
Variants that do not meet these criteria are set to NA.
}
\value{
The object returned is a \code{data.frame} with seven columns.
\describe{
\item{g00}{
Counts for genotype 00 (homozygous reference).
}
\item{g01}{
Counts for genotype 01 or 10 (heterozygous).
}
\item{g11}{
Counts for genotype 11 (homozygous alternate).
}
\item{a0Freq}{
Frequency of the reference allele.
}
\item{a1Freq}{
Frequency of the alternate allele.
}
\item{HWEzscore}{
Z-score for departure from a null hypothesis of Hardy Weinberg equilibrium.
}
\item{HWEpvalue}{
p-value for departure from a null hypothesis of Hardy Weinberg equilibrium.
}
}
}
\author{
Chris Wallace <cew54@cam.ac.uk>
}
\seealso{
\link{genotypeToSnpMatrix},
\link{probabilityToSnpMatrix}
}
\examples{
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
## The return value is a data.frame with genotype counts
## and allele frequencies.
df <- snpSummary(vcf)
df
## Compare to ranges in the VCF object:
rowRanges(vcf)
## No statistics were computed for the variants in rows 3, 4
## and 5. They were omitted because row 3 has two alternate
## alleles, row 4 has none and row 5 is not a SNP.
}
\keyword{manip}
|
