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\name{isSNV}
\alias{isSNV}
\alias{isInsertion}
\alias{isDeletion}
\alias{isIndel}
\alias{isTransition}
\alias{isSubstitution}
% VCF
\alias{isSNV,ExpandedVCF-method}
\alias{isSNV,CollapsedVCF-method}
\alias{isInsertion,ExpandedVCF-method}
\alias{isInsertion,CollapsedVCF-method}
\alias{isDeletion,ExpandedVCF-method}
\alias{isDeletion,CollapsedVCF-method}
\alias{isIndel,ExpandedVCF-method}
\alias{isIndel,CollapsedVCF-method}
\alias{isSubstitution,ExpandedVCF-method}
\alias{isSubstitution,CollapsedVCF-method}
\alias{isTransition,ExpandedVCF-method}
\alias{isTransition,CollapsedVCF-method}
% VRanges
\alias{isSNV,VRanges-method}
\alias{isInsertion,VRanges-method}
\alias{isDeletion,VRanges-method}
\alias{isIndel,VRanges-method}
\alias{isSubstitution,VRanges-method}
\alias{isTransition,VRanges-method}
\title{
Identification of genomic variant types.
}
\description{
Functions for identifying variant types such as SNVs, insertions,
deletions, transitions, and structural rearrangements.
}
\usage{
\S4method{isSNV}{VRanges}(x, ...)
\S4method{isSNV}{ExpandedVCF}(x, ...)
\S4method{isSNV}{CollapsedVCF}(x, ..., singleAltOnly = TRUE)
\S4method{isInsertion}{VRanges}(x, ...)
\S4method{isInsertion}{ExpandedVCF}(x, ...)
\S4method{isInsertion}{CollapsedVCF}(x, ..., singleAltOnly = TRUE)
\S4method{isDeletion}{VRanges}(x, ...)
\S4method{isDeletion}{ExpandedVCF}(x, ...)
\S4method{isDeletion}{CollapsedVCF}(x, ..., singleAltOnly = TRUE)
\S4method{isIndel}{VRanges}(x, ...)
\S4method{isIndel}{ExpandedVCF}(x, ...)
\S4method{isIndel}{CollapsedVCF}(x, ..., singleAltOnly = TRUE)
\S4method{isTransition}{VRanges}(x, ...)
\S4method{isTransition}{ExpandedVCF}(x, ...)
\S4method{isTransition}{CollapsedVCF}(x, ..., singleAltOnly = TRUE)
\S4method{isSubstitution}{VRanges}(x, ...)
\S4method{isSubstitution}{ExpandedVCF}(x, ...)
\S4method{isSubstitution}{CollapsedVCF}(x, ..., singleAltOnly = TRUE)
}
\arguments{
\item{x}{A \linkS4class{VCF} or \linkS4class{VRanges} object.
}
\item{singleAltOnly}{A \code{logical} only applicable when \code{x}
is a \link{CollapsedVCF} class.
When \code{TRUE} (default) only variants with a single alternate
allele are evaluated. When \code{FALSE} all ref / alt pairs for
each variant are evaluated. If any ref / alt pairs meet the
test criteria a value of TRUE is returned for the variant; this
may result in a value of TRUE for a variant with a mixture of
alternate alleles, some that pass the criteria and some that do not.
To retain single ref / alt pairs that pass the critera use
\code{expand} on the \code{CollapsedVCF} and then apply the test.
}
\item{\dots}{Arguments passed to other methods.
}
}
\details{
All functions return a logical vector the length of \code{x}.
\itemize{
\item{isSNV: }{
Reference and alternate alleles are both a single nucleotide long.
}
\item{isInsertion: }{
Reference allele is a single nucleotide and the alternate allele
is greater (longer) than a single nucleotide and the first
nucleotide of the alternate allele matches the reference.
}
\item{isDeletion: }{
Alternate allele is a single nucleotide and the reference allele
is greater (longer) than a single nucleotide and the first
nucleotide of the reference allele matches the alternate.
}
\item{isIndel: }{
The variant is either a deletion or insertion as determined
by \code{isDeletion} and \code{isInsertion}.
}
\item{isSubstition: }{
Reference and alternate alleles are the same length (1 or
more nucleotides long).
}
\item{isTransition: }{
Reference and alternate alleles are both a single nucleotide long.
The reference-alternate pair interchange is of either two-ring
purines (A <-> G) or one-ring pyrimidines (C <-> T).
}
}
}
\value{
A \code{logical} vector the same length as \code{x}.
}
\author{Michael Lawrence <mlawrence@gene.com> and
Valerie Obenchain <vobencha@fhcrc.org>}
\examples{
fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
## ---------------------------------------------------------------------
## VCF objects
## ---------------------------------------------------------------------
vcf <- readVcf(fl, "hg19")
DataFrame(ref(vcf), alt(vcf))
## This vcf has transitions in row 2 and 3. When 'singleAltOnly=TRUE'
## only the row 2 variant is identified:
isTransition(vcf)
## Both row 2 and 3 are identified when 'singleAltOnly=FALSE':
isTransition(vcf, singleAltOnly=FALSE)
## Expand the CollapsedVCF to ExpandedVCF
evcf <- expand(vcf)
## All ref / alt pairs are now expanded and there is no need to
## use 'singleAltOnly'. The return length is now 7 instead of 5:
transition <- isTransition(evcf)
transition
DataFrame(ref(evcf)[transition], alt(evcf)[transition])
## ---------------------------------------------------------------------
## VRanges objects
## ---------------------------------------------------------------------
## A VRanges object holds data from a VCF class in a completely
## 'flat' fashion. INFO and FORMAT variables for all subjects are
## 'repped' out such that each row is a unique combination of data.
vr <- as(vcf, "VRanges")
isSNV(vr, singleAltOnly=FALSE)
}
\keyword{methods}
|
