rle.query: Queries an 'RleList' representing genomic data

In mskilab/gUtils: R Package Providing Additional Capabilities and Speed for GenomicRanges Operations

Queries an RleList representing genomic data

Description

Queries an RleList representing genomic data

(i.e. a list whose names represent seqnames ie chromosomes, and lengths represent seqlengths) via GRanges object

Usage

rle.query(
  subject.rle,
  query.gr,
  chunksize = 1e+09,
  mc.cores = 1,
  verbose = FALSE
)

Arguments

subject.rle	Rle
query.gr	integer GRangeslist or GRanges
chunksize	integer Number of query.gr ranges to consider in one memory chunk. (default = 1e9)
mc.cores	Number of cores to apply when doing chunked operation (default = 1)
verbose	boolean Set the verbosity of the output (default = FALSE)

Value

Rle representing the (concatenated) vector of data (reversing order in case of negative strand input)

Note

Throws warning if seqlengths(gr) do not correspond to the lengths of the RleList components

mskilab/gUtils documentation built on June 6, 2023, 12:08 a.m.