seq2fft: seq2fft

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

seq2fft

Description

Creates ffTrack object from BSGenome or FASTA (coming soon) file

## will either convert (1) raw sequence (2) k-nucleotide context centered around base or (3) motifs defined by some dictionary (anchored at first base) into leveled ffTrack (i.e. integer track with populated levels field)

Usage

seq2fft(seq, fftpath, nnuc = 0, dict = NULL, chrsub = TRUE, neg = FALSE,
  region = NULL, mc.cores = 1, verbose = FALSE, buffer = 1e+05,
  skip.sweep = FALSE, vmode = "ubyte", min.gapwidth = 1000)

Arguments

seq	BSGenome object, ffTrack object representing genomic sequence, or (not yet supported) FASTA file
fftpath	path to ffTrack .rds that will be created by this
nnuc	how many nucleotides to left and right to enumerate
dict	this should be a character vector or DNAStringSet, overrides nnuc arg if not null
chrsub	whether to sub in / sub out 'chr' when accessing seq file
neg	whether to analyze sequence data on negative strand (i.e. motifs will be analyzed in rev complement)
region	GRanges specifying regions to limit ffTrack computation to (default is whole genome, ie seqnames of BigWig file)
mc.cores	currently mc.cores can only be one (weird mclapply bug when running)
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 specifyhing vmode to use for encoding (by default double)
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)

Value

ffTrack object corresponding to the data in the BigWig file

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