gviz_utils: Generic internal functions used by genespace

In jtlovell/GENESPACE: Synteny- and orthology-constrained comparative genomics

Generic internal functions used by genespace

Description

gviz_utils Convenience functions for gscTools, not meant to be called directly by the user. Little documentation support provided, use at your own risk.

join_ranges join_ranges

pull_seqInfo pull_seqInfo

find_gaps find_gaps

subset_bedInGap subset_bedInGap

get_gappedRanges get_gappedRanges

convert_si2gr convert_si2gr

rename_chrs Parse common formats for chromosomes, specifically splitting whitespace separated fields and finding the field like to give the chromosome ID

Usage

join_ranges(bed, seqInfo)

pull_seqInfo(dnass)

find_gaps(gr)

subset_bedInGap(gr, gapGr)

get_gappedRanges(existingGr, newGr)

convert_si2gr(seqInfo)

rename_chrs(dnass)

Arguments

bed	data.table or data.frame with at least chr, start, end columns
seqInfo	seqInfo ranges extracted from dnass
dnass	DNAStringSet
gr	granges object
gapGr	granges with gaps If called, gviz_utils returns its own arguments.
existingGr	existing granges to mask with
newGr	new granges to mask

jtlovell/GENESPACE documentation built on Jan. 25, 2025, 6:39 a.m.