getSexFromVcf.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/getSex.R
\name{getSexFromVcf}
\alias{getSexFromVcf}
\title{Get sample sex from a VCF file}
\usage{
getSexFromVcf(
  vcf,
  tumor.id.in.vcf = NULL,
  min.or = 4,
  min.or.na = 2.5,
  max.pv = 0.001,
  homozygous.cutoff = 0.95,
  af.cutoff = 0.2,
  min.coverage = 15,
  use.somatic.status = TRUE
)
}
\arguments{
\item{vcf}{CollapsedVCF object, read in with the \code{readVcf} function
from the VariantAnnotation package.}

\item{tumor.id.in.vcf}{The tumor id in the CollapsedVCF (optional).}

\item{min.or}{Minimum odds-ratio to call sample as male. If p-value is not
significant due to a small number of SNPs on chromosome X, sample will be
called as NA even when odds-ratio exceeds this cutoff.}

\item{min.or.na}{Minimum odds-ratio to not call a sample. Odds-ratios in the
range \code{min.or.na} to \code{min.or} define a grey area in which samples
are not called. Contamination can be a source of ambiguous calls.}

\item{max.pv}{Maximum Fisher's exact p-value to call sample as male.}

\item{homozygous.cutoff}{Minimum allelic fraction to call position
homozygous.}

\item{af.cutoff}{Remove all SNVs with allelic fraction lower than the
specified value.}

\item{min.coverage}{Minimum coverage in tumor. Variants with lower coverage
are ignored.}

\item{use.somatic.status}{If somatic status and germline data is available,
then exclude somatic variants.}
}
\value{
Returns a \code{character(1)} with \code{M} for male, \code{F} for
female, or \code{NA} if unknown.
}
\description{
This function detects non-random distribution of homozygous variants on
chromosome X compared to all other chromosomes. A non-significant Fisher's
exact p-value indicates more than one chromosome X copy. This function is
called in runAbsoluteCN as sanity check when a VCF is provided. It is also
useful for determining sex when no sex marker genes on chrY (e.g. AMELY) are
available.
}
\examples{

vcf.file <- system.file("extdata", "example.vcf.gz", package = "PureCN")
vcf <- readVcf(vcf.file, "hg19")
# This example vcf is filtered and contains no homozygous calls,
# which are necessary for determining sex from chromosome X.
getSexFromVcf(vcf)

}
\seealso{
\code{\link{getSexFromCoverage}}
}
\author{
Markus Riester
}