R: Finding overlapping genomic alignments

findOverlaps-methods {GenomicAlignments}

R Documentation

Finding overlapping genomic alignments

Description

Finds range overlaps between a GAlignments, GAlignmentPairs, or GAlignmentsList object, and another range-based object.

NOTE: The findOverlaps generic function and methods for Ranges and RangesList objects are defined and documented in the IRanges package. The methods for GRanges and GRangesList objects are defined and documented in the GenomicRanges package.

Usage

## S4 method for signature 'GAlignments,GAlignments'
findOverlaps(query, subject,
    maxgap=0L, minoverlap=1L,
    type=c("any", "start", "end", "within"),
    select=c("all", "first", "last", "arbitrary"),
    algorithm=c("nclist", "intervaltree"),
    ignore.strand=FALSE)

## S4 method for signature 'GAlignments,GAlignments'
countOverlaps(query, subject,
    maxgap=0L, minoverlap=1L,
    type=c("any", "start", "end", "within"),
    algorithm=c("nclist", "intervaltree"),
    ignore.strand=FALSE)

## S4 method for signature 'GAlignments,GAlignments'
overlapsAny(query, subject,
    maxgap=0L, minoverlap=1L,
    type=c("any", "start", "end", "within"),
    algorithm=c("nclist", "intervaltree"),
    ignore.strand=FALSE)

## S4 method for signature 'GAlignments,GAlignments'
subsetByOverlaps(query, subject,
    maxgap=0L, minoverlap=1L,
    type=c("any", "start", "end", "within"),
    algorithm=c("nclist", "intervaltree"),
    ignore.strand=FALSE)

Arguments

`query, subject`	A GAlignments, GAlignmentPairs, or GAlignmentsList object for either `query` or `subject`. A vector-like object containing ranges for the other one.
`maxgap, minoverlap, type, select, algorithm`	See `findOverlaps` in the IRanges package for a description of these arguments.
`ignore.strand`	When set to `TRUE`, the strand information is ignored in the overlap calculations.

Details

When the query or the subject (or both) is a GAlignments object, it is first turned into a GRangesList object (with as( , "GRangesList")) and then the rules described previously apply. GAlignmentsList objects are coerced to GAlignments then to a GRangesList. Feature indices are mapped back to the original GAlignmentsList list elements.

When the query is a GAlignmentPairs object, it is first turned into a GRangesList object (with as( , "GRangesList")) and then the rules described previously apply.

Value

For findOverlaps either a Hits object when select = "all" or an integer vector otherwise.

For countOverlaps an integer vector containing the tabulated query overlap hits.

For overlapsAny a logical vector of length equal to the number of ranges in query indicating those that overlap any of the ranges in subject.

For subsetByOverlaps an object of the same class as query containing the subset that overlapped at least one entity in subject.

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)

[Package GenomicAlignments version 1.4.1 Index]