findOverlapsGRL: Find overlaps between two GRangesList objects

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

Find overlaps between two GRangesList objects

Description

Find overlaps between two GRangesList objects

Usage

findOverlapsGRL(
  GRL1,
  GRL2,
  annoName1 = "name",
  annoName2 = "name",
  check_names = TRUE,
  ...
)

Arguments

GRL1	GRangesList query
GRL2	GRangesList subject
annoName1	character value indicating either the colname of values(GRL1) to use as the name, or if "name" then it uses names(GRL1).
annoName2	character value indicating either the colname of values(GRL2) to use as the name, or if "name" then it uses names(GRL2).
check_names	logical indicating whether the values defined by annoName1 should match the values defined by annoName2. Note that when check_names=FALSE the overlaps returned will depend upon GRL1 and GRL2 being in identical order. Otherwise, the values in annoName1 and annoName2 are used, which means GRL1 and GRL2 do not have to be in identical order.
...	additional arguments are passed to GenomicRanges::findOverlaps(), useful for customizing the overlap criteria.

Details

This function implements GenomicRanges::findOverlaps() for the special case of two GRangesList objects, restricting results to those including the same GRangesList index in the subject and query.

Value

Hits object, or the natural output from GenomicRanges::findOverlaps() dependent upon the ... arguments, subsetted for only entries with matching values defined by annoName1 and annoName2.

See Also

Other jam GRanges functions: addGRLgaps(), addGRgaps(), annotateGRLfromGRL(), annotateGRfromGR(), assignGRLexonNames(), closestExonToJunctions(), combineGRcoverage(), exoncov2polygon(), flattenExonsBy(), getFirstStrandedFromGRL(), getGRLgaps(), getGRcoverageFromBw(), getGRgaps(), grl2df(), jam_isDisjoint(), make_ref2compressed(), sortGRL(), spliceGR2junctionDF(), stackJunctions()

Other jam GRanges functions: addGRLgaps(), addGRgaps(), annotateGRLfromGRL(), annotateGRfromGR(), assignGRLexonNames(), closestExonToJunctions(), combineGRcoverage(), exoncov2polygon(), flattenExonsBy(), getFirstStrandedFromGRL(), getGRLgaps(), getGRcoverageFromBw(), getGRgaps(), grl2df(), jam_isDisjoint(), make_ref2compressed(), sortGRL(), spliceGR2junctionDF(), stackJunctions()

jmw86069/splicejam documentation built on April 14, 2025, 3:12 a.m.