getGRgaps: Get gaps in GRanges

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

Get gaps in GRanges

Description

Get gaps in GRanges

Usage

getGRgaps(gr, strandSpecific = TRUE, verbose = FALSE, ...)

Arguments

gr	GRanges object
strandSpecific	logical indicating whether to convert strand to "*" prior to determining gaps between features.
verbose	logical indicating whether to print verbose output.
...	additional arguments are passed to getGRLgaps().

Details

This function returns the gaps between GRanges regions, calculated for each chromosome (using GenomicRanges::seqnames(gr)), and when strandSpecific=TRUE it determines gaps in stranded fashion.

See Also

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

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