get_seqLen: Get sequence lengths for chromosomes/scaffolds

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Get sequence lengths for chromosomes/scaffolds

Description

Get sequence lengths for chromosomes/scaffolds from a BSgenome::BSgenome object

Usage

get_seqLen(genome = getInPASGenome(), chr2exclude = getChr2Exclude())

Arguments

genome	An object of BSgenome::BSgenome
chr2exclude	A character vector, NA or NULL, specifying chromosomes or scaffolds to be excluded for InPAS analysis. chrM and alternative scaffolds representing different haplotypes should be excluded.

Value

A named numeric vector containing lengths per seqname, with the seqnames as the names

Author(s)

Jianhong Ou, Haibo Liu

See Also

GenomeInfoDb::Seqinfo

Examples

library(BSgenome.Mmusculus.UCSC.mm10)
genome <- BSgenome.Mmusculus.UCSC.mm10
InPAS:::get_seqLen(
  genome = genome,
  chr2exclude = "chrM"
)

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.