hg_seqlengths: Output standard human genome seqlengths

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

Output standard human genome seqlengths

Description

Outputs a standard seqlengths for human genome +/- "chr".

Usage

hg_seqlengths(genome = NULL, chr = TRUE, include.junk = FALSE)

Arguments

genome	A BSgenome or object with a seqlengths accessor. Default is hg19, but loads with warning unless explicitly provided
chr	boolean Flag for whether to keep "chr". (default = FALSE)
include.junk	boolean Flag for whether to not trim to only 1-22, X, Y, M. (default = FALSE)

Value

Named integer vector with elements corresponding to the genome seqlengths

Note

A default genome can be set with the environment variable DEFAULT_GENOME. This can be the full namespace of the genome e.g.: DEFAULT_GENOME=BSgenome.Hsapiens.UCSC.hg19::Hsapiens OR a URL / file path pointing to a chrom.sizes text file (e.g. http://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes) specifying a genome definition

Author(s)

Marcin Imielinski

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