bw2fft: bw2fft

In mskilab/ffTrack: GenomicRanges-based R package for fast, out-of-core memory access and storage of genomic data using ff

bw2fft

Description

Creates ffTrack object from input bigwig file.

Usage

bw2fft(bwpath, fftpath = gsub("(\\.bw.*)|(\\.bigwig.*)", ".rds", bwpath),
  region = NULL, chrsub = TRUE, verbose = FALSE, buffer = 1e+05,
  skip.sweep = FALSE, vmode = "double", resume = FALSE,
  min.gapwidth = 1000, overwrite = FALSE, mc.cores = 1)

Arguments

bwpath	path to BigWig
fftpath	path to ffTrack .rds that will be created by this (by default .bw is replaced by .rds)
region	GRanges specifying regions to limit ffTrack computation to (default is whole genome, ie seqnames of BigWig file); whether to limit to certain region (instead of whole genome)
chrsub	whether to sub out 'chr' in seqnames / seqlevels of BigWig object; whether to sub in / sub out 'chr' when accessing bigwig file
verbose	logical flag
buffer	integer size of how big of a buffer to use when transferring data from BigWig to ffTrack object; number of bases to access at a time
skip.sweep	logical flag (default FALSE) if TRUE will skip the sweep of "region" for the portions that have non-NA values; if TRUE will not sweep for covered region, just make a whole genome file or a file across provided regions
vmode	character specifying vmode to use for encoding (default == 'double')
resume	logical flag specifying whether to resume the populatino of an already existing ffTrack object (default FALSE)
min.gapwidth	minimum gap-width with which to merge reference adjacent intervals, this will mildly increase the file size but reduce the range complexity of the GRanges object; flank (to reduce the range complexity of the ffdata skeleton, but increase file size)
overwrite	boolean Flag whether to overwrite existing in the filename
mc.cores	integer Number of cores to use via parallel::mclapply

Value

ffTrack object corresponding to the data in the BigWig file

Author(s)

Marcin Imielinski

mskilab/ffTrack documentation built on Feb. 6, 2023, 2:47 a.m.