trim_seqnames: Filter sequence names from a BSgenome object

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

Filter sequence names from a BSgenome object

Description

Filter sequence names for scaffolds from a BSgenome object so that only chromosome-level seqnames are kept.

Usage

trim_seqnames(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

An character vector containing filtered seqnames

Author(s)

Jianhong Ou, Haibo Liu

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