gr.fix: "Fixes" 'seqlengths' / 'seqlevels'

In mskilab/gUtils: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

"Fixes" seqlengths / seqlevels

Description

If "genome" not specified will replace NA seqlengths in GRanges to reflect largest coordinate per seqlevel and removes all NA seqlevels after this fix.

If "genome" defined (i.e. as Seqinfo object, or a BSgenome, GRanges, GRangesList object with populated seqlengths), then will replace seqlengths in gr with those for that genome

Usage

gr.fix(gr, genome = NULL, gname = NULL, drop = FALSE, pruning.mode = "coarse")

Arguments

gr	GRanges object to fix
genome	Genome to fix to: Seqinfo, BSgenome, GRanges (w/seqlengths), GRangesList (w/seqlengths) (default = NULL)
gname	string Name of the genome (optional, just appends to Seqinfo of the output) (default = NULL)
drop	boolean Remove ranges that are not present in the supplied genome (default = FALSE)
pruning.mode	string Controls how to prune x. Four pruning modes are currently defined: "error", "coarse", "fine", and "tidy". See GenomeInfoDb documentation.

Value

GRanges pile with the fixed Seqinfo

mskilab/gUtils documentation built on June 6, 2023, 12:08 a.m.