seqIdStartEnd2GRanges: Make GRanges

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Make GRanges

Description

Return a GRanges object from sequence identifiers, starts and ends.

Usage

seqIdStartEnd2GRanges(
  seq.id,
  seq.start = NULL,
  seq.end = NULL,
  dict.file = NULL,
  subseq.name = NULL
)

Arguments

seq.id	sequence identifier(s) to work on (e.g. "chr2" or c("chr2","chr7"))
seq.start	start(s) of the sequence(s) to work on (if NULL, whole seq; see dict.file)
seq.end	end(s) of the sequence(s) to work on (if NULL, whole seq; see dict.file)
dict.file	path to the SAM dict file (see https://broadinstitute.github.io/picard/command-line-overview.html#CreateSequenceDictionary) if seq.id is specified with no start/end
subseq.name	names of the subsequence(s) (optional; e.g. "gene34" or "snp005")

Value

GRanges object from the GenomicRanges package

Author(s)

Timothee Flutre

See Also

vcf2dosage, vcf2genoClasses

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.