CleanupGRanges: Cleanup genomic ranges

In benja0x40/Tightrope: ChIP-seq normalization according to background reads density

Description

Cleanup genomic ranges such as imported ChIP-seq peaks from bed files by removing ranges corresponding to non canonical chromosomes.

Usage

CleanupGRanges(grg, seqinfo, organism, blacklist = NULL,
  keep.strand = FALSE)

Arguments

grg	a GRanges object.
seqinfo	Seqinfo object for the considered organism.
organism	name of the organism (e.g. "Homo sapiens", "Mus musculus").
blacklist	an optional GRanges object used to filter out any genomic ranges overlaping with the blacklisted one (default = NULL, none).
keep.strand	logical, when TRUE strand information is retained, when FALSE (default) strand information is discarded (i.e. strand = "*").

Value

CleanupGRanges returns a GRanges object.

See Also

ImportGenomicRanges, ImportCpGIslandExt

benja0x40/Tightrope documentation built on May 24, 2019, 1:35 a.m.