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\name{findOverlaps-methods}
\alias{findOverlaps-methods}
\alias{findOverlaps}
\alias{findOverlaps,GAlignments,Vector-method}
\alias{findOverlaps,Vector,GAlignments-method}
\alias{findOverlaps,GAlignments,GAlignments-method}
\alias{findOverlaps,GAlignments,GRangesList-method}
\alias{findOverlaps,GRangesList,GAlignments-method}
\alias{findOverlaps,GAlignmentPairs,Vector-method}
\alias{findOverlaps,Vector,GAlignmentPairs-method}
\alias{findOverlaps,GAlignmentPairs,GAlignmentPairs-method}
\alias{findOverlaps,GAlignmentsList,Vector-method}
\alias{findOverlaps,Vector,GAlignmentsList-method}
\alias{findOverlaps,GAlignmentsList,GAlignmentsList-method}
\alias{countOverlaps}
\alias{countOverlaps,GAlignments,Vector-method}
\alias{countOverlaps,Vector,GAlignments-method}
\alias{countOverlaps,GAlignments,GAlignments-method}
\alias{countOverlaps,GAlignments,GenomicRanges-method}
\alias{countOverlaps,GenomicRanges,GAlignments-method}
\alias{countOverlaps,GAlignments,GRangesList-method}
\alias{countOverlaps,GRangesList,GAlignments-method}
\alias{countOverlaps,GAlignmentPairs,Vector-method}
\alias{countOverlaps,Vector,GAlignmentPairs-method}
\alias{countOverlaps,GAlignmentPairs,GAlignmentPairs-method}
\alias{countOverlaps,GAlignmentsList,Vector-method}
\alias{countOverlaps,Vector,GAlignmentsList-method}
\alias{countOverlaps,GAlignmentsList,GAlignmentsList-method}
\alias{overlapsAny}
\alias{overlapsAny,GAlignments,Vector-method}
\alias{overlapsAny,Vector,GAlignments-method}
\alias{overlapsAny,GAlignments,GAlignments-method}
\alias{overlapsAny,GAlignmentPairs,Vector-method}
\alias{overlapsAny,Vector,GAlignmentPairs-method}
\alias{overlapsAny,GAlignmentPairs,GAlignmentPairs-method}
\alias{overlapsAny,GAlignmentsList,Vector-method}
\alias{overlapsAny,Vector,GAlignmentsList-method}
\alias{overlapsAny,GAlignmentsList,GAlignmentsList-method}
\alias{subsetByOverlaps}
\alias{subsetByOverlaps,GAlignments,Vector-method}
\alias{subsetByOverlaps,Vector,GAlignments-method}
\alias{subsetByOverlaps,GAlignments,GAlignments-method}
\alias{subsetByOverlaps,GAlignmentPairs,Vector-method}
\alias{subsetByOverlaps,Vector,GAlignmentPairs-method}
\alias{subsetByOverlaps,GAlignmentPairs,GAlignmentPairs-method}
\alias{subsetByOverlaps,GAlignmentsList,Vector-method}
\alias{subsetByOverlaps,Vector,GAlignmentsList-method}
\alias{subsetByOverlaps,GAlignmentsList,GAlignmentsList-method}
\title{Finding overlapping genomic alignments}
\description{
Finds range overlaps between a \link{GAlignments}, \link{GAlignmentPairs},
or \link{GAlignmentsList} object, and another range-based object.
NOTE: The \code{\link[IRanges]{findOverlaps}} generic function and methods
for \link[IRanges]{Ranges} and \link[IRanges]{RangesList} objects
are defined and documented in the \pkg{IRanges} package.
The methods for \link[GenomicRanges]{GRanges} and
\link[GenomicRanges]{GRangesList} objects are defined and
documented in the \pkg{GenomicRanges} package.
}
\usage{
\S4method{findOverlaps}{GAlignments,GAlignments}(query, subject,
maxgap = 0L, minoverlap = 1L,
type = c("any", "start", "end", "within"),
select = c("all", "first"),
ignore.strand = FALSE)
\S4method{countOverlaps}{GAlignments,GAlignments}(query, subject,
maxgap = 0L, minoverlap = 1L,
type = c("any", "start", "end", "within"),
ignore.strand = FALSE)
\S4method{overlapsAny}{GAlignments,GAlignments}(query, subject,
maxgap = 0L, minoverlap = 1L,
type = c("any", "start", "end", "within"),
ignore.strand = FALSE)
\S4method{subsetByOverlaps}{GAlignments,GAlignments}(query, subject,
maxgap = 0L, minoverlap = 1L,
type = c("any", "start", "end", "within"),
ignore.strand = FALSE)
}
\arguments{
\item{query, subject}{
A \link{GAlignments}, \link{GAlignmentPairs}, or \link{GAlignmentsList}
object for either \code{query} or \code{subject}.
A vector-like object containing ranges for the other one.
}
\item{maxgap, minoverlap, type, select}{
See \code{\link[IRanges]{findOverlaps}} in the \pkg{IRanges} package
for a description of these arguments.
}
\item{ignore.strand}{
When set to \code{TRUE}, the strand information is ignored in the
overlap calculations.
}
}
\details{
When the query or the subject (or both) is a \link{GAlignments}
object, it is first turned into a \link{GRangesList} object (with
\code{as( , "GRangesList")}) and then the rules described previously
apply. \link{GAlignmentsList} objects are coerced to \link{GAlignments}
then to a \link{GRangesList}. Feature indices are mapped back to the
original \link{GAlignmentsList} list elements.
When the query is a \link{GAlignmentPairs} object, it is first
turned into a \link{GRangesList} object (with \code{as( , "GRangesList")})
and then the rules described previously apply.
}
\value{
For \code{findOverlaps} either a \link[IRanges]{Hits} object when
\code{select = "all"} or an integer vector otherwise.
For \code{countOverlaps} an integer vector containing the tabulated
query overlap hits.
For \code{overlapsAny} a logical vector of length equal to the number of
ranges in \code{query} indicating those that overlap any of the ranges
in \code{subject}.
For \code{subsetByOverlaps} an object of the same class as \code{query}
containing the subset that overlapped at least one entity in \code{subject}.
}
\seealso{
\itemize{
\item \code{\link[IRanges]{findOverlaps}}.
\item \link[IRanges]{Hits-class}.
\item \link{GRanges-class}.
\item \link{GRangesList-class}.
\item \link{GAlignments-class}.
\item \link{GAlignmentPairs-class}.
\item \link{GAlignmentsList-class}.
}
}
\examples{
ex1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
galn <- readGAlignments(ex1_file)
subject <- granges(galn)[1]
## Note the absence of query no. 9 (i.e. 'galn[9]') in this result:
as.matrix(findOverlaps(galn, subject))
## This is because, by default, findOverlaps()/countOverlaps() are
## strand specific:
galn[8:10]
countOverlaps(galn[8:10], subject)
countOverlaps(galn[8:10], subject, ignore.strand=TRUE)
## Count alignments in 'galn' that DO overlap with 'subject' vs those
## that do NOT:
table(overlapsAny(galn, subject))
## Extract those that DO:
subsetByOverlaps(galn, subject)
## GAlignmentsList
galist <- GAlignmentsList(galn[8:10], galn[3000:3002])
gr <- GRanges(c("seq1", "seq1", "seq2"),
IRanges(c(15, 18, 1233), width=1),
strand=c("-", "+", "+"))
countOverlaps(galist, gr)
countOverlaps(galist, gr, ignore.strand=TRUE)
findOverlaps(galist, gr)
findOverlaps(galist, gr, ignore.strand=TRUE)
}
\keyword{methods}
\keyword{utilities}
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