trim_seqnames {InPAS}R Documentation

Filter the sequence names from a BSgenome object

Description

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

Usage

trim_seqnames(genome, removeScaffolds = FALSE)

Arguments

genome

An object of BSgenome::BSgenome

removeScaffolds

A logical(1) vector, whether the scaffolds should be removed from the genome If you use a TxDb containing alternative scaffolds, you'd better to remove the scaffolds. To make things easy, we suggest users creating a BSgenome::BSgenome instance from the reference genome used for read alignment. For details, see the documentation of BSgenome::forgeBSgenomeDataPkg().

Value

An character vector containing filtered seqnames

Author(s)

Jianhong Ou, Haibo Liu


[Package InPAS version 2.1.0 Index]