getGRLgaps: Get gaps in GRangesList objects

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

Get gaps in GRangesList objects

Description

Get gaps in GRangesList objects

Usage

getGRLgaps(grl, strandSpecific = TRUE, verbose = FALSE, ...)

Arguments

grl	GRangesList object.
strandSpecific	logical indicating whether to determine gaps within strand.
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Details

This function returns gaps between GRanges regions in a GRangesList object. When strandSpecific=TRUE is determines gaps per strand, otherwise strands are converted to "*". It will also determine gaps within chromosome for each GRanges entry in GRangesList.

Value

GRangesList object with gaps for each chromosome and strand present in each GRanges entry. It does not return gap sequence at the edges of GRanges regions to the chromosome ends.

See Also

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

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.