utils: Generic internal functions used by genespace

In jtlovell/gscTools: Genome exploration R tools

Generic internal functions used by genespace

Description

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

.onAttach startup messages

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

.onAttach(...)

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

...	additional arguments passed on If called, utils returns its own 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
existingGr	existing granges to mask with
newGr	new granges to mask
kmers	DNAStringSet with kmers to find
nCores	integer, then number of cores to use
x	single-value parameter, string, integer, numeric, list, vector

jtlovell/gscTools documentation built on March 16, 2023, 10:24 p.m.