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\name{findCompatibleOverlaps-methods}
\alias{findCompatibleOverlaps-methods}
\alias{findCompatibleOverlaps}
\alias{findCompatibleOverlaps,GAlignments,GRangesList-method}
\alias{findCompatibleOverlaps,GAlignmentPairs,GRangesList-method}
\alias{countCompatibleOverlaps}
\title{Finding hits between reads and transcripts that are \emph{compatible}
with the splicing of the transcript}
\description{
In the context of an RNA-seq experiment, \code{findCompatibleOverlaps}
(or \code{countCompatibleOverlaps}) can be used for finding (or counting)
hits between reads and transcripts that are \emph{compatible}
with the splicing of the transcript.
}
\usage{
findCompatibleOverlaps(query, subject)
countCompatibleOverlaps(query, subject)
}
\arguments{
\item{query}{
A \link{GAlignments} or \link{GAlignmentPairs} object representing
the aligned reads.
}
\item{subject}{
A \link{GRangesList} object representing the transcripts.
}
}
\details{
\code{findCompatibleOverlaps} is a specialized version of
\code{\link[IRanges]{findOverlaps}} that uses
\code{\link{encodeOverlaps}} internally to keep only
the hits where the junctions in the aligned read are \emph{compatible}
with the splicing of the annotated transcript.
The topic of working with overlap encodings is covered in details
in the "OverlapEncodings" vignette located this package
(\pkg{GenomicAlignments}) and accessible with
\code{vignette("OverlapEncodings")}.
}
\value{
A \link[IRanges]{Hits} object for \code{findCompatibleOverlaps}.
An integer vector \emph{parallel} to (i.e. same length as) \code{query}.
}
\author{
H. Pages
}
\seealso{
\itemize{
\item The \code{\link[IRanges]{findOverlaps}} generic function defined
in the \pkg{IRanges} package.
\item The \code{\link{encodeOverlaps}} generic function and
\link{OverlapEncodings} class.
\item The "OverlapEncodings" vignette in this package.
\item \link{GAlignments} and \link{GAlignmentPairs} objects.
\item \link[GenomicRanges]{GRangesList} objects in the
\pkg{GenomicRanges} package.
}
}
\examples{
## Here we only show a simple example illustrating the use of
## countCompatibleOverlaps() on a very small data set. Please
## refer to the "OverlapEncodings" vignette in the GenomicAlignments
## package for a comprehensive presentation of "overlap
## encodings" and related tools/concepts (e.g. "compatible"
## overlaps, "almost compatible" overlaps etc...), and for more
## examples.
## sm_treated1.bam contains a small subset of treated1.bam, a BAM
## file containing single-end reads from the "Pasilla" experiment
## (RNA-seq, Fly, see the pasilla data package for the details)
## and aligned to reference genome BDGP Release 5 (aka dm3 genome on
## the UCSC Genome Browser):
sm_treated1 <- system.file("extdata", "sm_treated1.bam",
package="GenomicAlignments", mustWork=TRUE)
## Load the alignments:
flag0 <- scanBamFlag(isDuplicate=FALSE, isNotPassingQualityControls=FALSE)
param0 <- ScanBamParam(flag=flag0)
gal <- readGAlignments(sm_treated1, use.names=TRUE, param=param0)
## Load the transcripts (IMPORTANT: Like always, the reference genome
## of the transcripts must be *exactly* the same as the reference
## genome used to align the reads):
library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
exbytx <- exonsBy(TxDb.Dmelanogaster.UCSC.dm3.ensGene, by="tx", use.names=TRUE)
## Number of "compatible" transcripts per alignment in 'gal':
gal_ncomptx <- countCompatibleOverlaps(gal, exbytx)
mcols(gal)$ncomptx <- gal_ncomptx
table(gal_ncomptx)
mean(gal_ncomptx >= 1)
## --> 33% of the alignments in 'gal' are "compatible" with at least
## 1 transcript in 'exbytx'.
## Keep only alignments compatible with at least 1 transcript in
## 'exbytx':
compgal <- gal[gal_ncomptx >= 1]
head(compgal)
}
\keyword{methods}
\keyword{utilities}
|
