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 2.2.0 Index]