get_genome: Get genome

In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

Get genome

Description

Get a genome (or a subset of chromosomes from a genome) as a GRanges object. This can be useful for querying whole-chromosomes at a time.

Usage

get_genome(
  keep.chr = paste0("chr", c(seq_len(22), "X", "Y")),
  genome = "hg19",
  sort = TRUE,
  style = "UCSC",
  split_chromosomes = FALSE
)

Arguments

keep.chr	is a character vector stating the names of the chromosomes to keep. Any chromosome not in the vector will be filtered out. If keep.chr is supplied, organism and chr.type are ignored.
genome	The genome object or genome identifier.
sort	Whether to sort the GRanges by chromosomes.
style	Chromosome style, set by seqlevelsStyle. "UCSC" : Uses the chromosome style "chr1". "NCBI" : Uses the chromosome style "1"
split_chromosomes	Whether to split the GRanges by chromosome (as a named list).

Value

GRanges

Examples

gr <- get_genome(keep.chr=1:2)

neurogenomics/PeakyFinders documentation built on Oct. 14, 2024, 3:09 p.m.