get_seqLen {InPAS} | R Documentation

## Get sequence lengths for chromosomes/scaffolds

### Description

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

### Usage

    get_seqLen(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

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, removeScaffolds = FALSE)

[Package InPAS version 2.2.0 Index]