grl.span: grl.span

In mskilab/skitools: Various mskilab R utilties

grl.span

Description

Returns GRanges object representing the left / right extent of each GRL item. In case of "chimeric" GRL items (ie that map to two chromosomes) there are two options: (1) specify "chr" chromosome as argument to subset GRL's that are on that chromosome, and compute GRL extents from this, any GRL full outside of that chromosome will get a 0 width GRL (2) (default) allow chimeric GRL items to get an extent that is with respect to the first chromosome in that GRL

Usage

grl.span(grl, chr = NULL, ir = FALSE, keep.strand = TRUE)

Arguments

grl	GRangesList to query
chr	[Default NULL]
ir	[Default FALSE]
keep.strand	[Default TRUE]

Details

If a grl item contains ranges that lie on different chromosomes, then corresponding grange will have chromosome "NA" and IRange(0, 0)

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.