wig2fft: wig2fft

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

wig2fft

Description

Creates ffTrack object from input .wig file

Usage

wig2fft(wigpath, fftpath = gsub("(\\.wig.*)", ".rds", wigpath),
  chrsub = TRUE, verbose = FALSE, buffer = 1e+05, skip.sweep = FALSE,
  seqlengths = hg_seqlengths(), vmode = "double", gz = grepl("\\.gz$",
  wigpath), bz2 = grepl("\\.bz2$", wigpath), min.gapwidth = 1000,
  overwrite = FALSE)

Arguments

wigpath	path to Wig
fftpath	path to ffTrack .rds that will be created by this (by default .bw is replaced by .rds)
chrsub	whether to sub out 'chr' in seqnames / seqlevels of Wig object
verbose	logical flag
buffer	integer size of how big of a buffer to use when transferring data from Wig 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
seqlengths	info
vmode	character specifyhing vmode to use for encoding (by default double)
gz	stuff
bz2	stuff
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

Value

ffTrack object corresponding to the data in the Wig file

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