get_seq: get_seq

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

get_seq

Description

Retrieve genomic sequences

Wrapper around getSeq which does the "chr" and seqnames conversion if necessary also handles GRangesList queries

Usage

get_seq(
  hg,
  gr,
  unlist = TRUE,
  mc.cores = 1,
  mc.chunks = mc.cores,
  add.chr = FALSE,
  as.data.table = FALSE,
  verbose = FALSE
)

Arguments

hg	A BSgenome or and ffTrack object with levels = c('A','T','G','C','N')
gr	GRanges object to define the ranges
unlist	logical whether to unlist the final output into a single DNAStringSet. (default = TRUE)
mc.cores	Optional multicore call. (default = 1)
mc.chunks	Optional define how to chunk the multicore call. (default = mc.cores)
as.data.table	boolean (default = FALSE)
verbose	boolean Flag to increase verbosity (default = FALSE)

Value

DNAStringSet of sequences

mskilab/ffTrack documentation built on June 15, 2025, 2:51 p.m.