R: Retrieve reference sequence from a BAM file as data.frame

getRefData {rbamtools} | R Documentation

## Retrieve reference sequence from a BAM file as data.frame

### Description

The four functions: `getRefCoords`, `getRefCount`, `getRefData` and `getRefId` provide reading access to data about the present reference sequences in bamReader or bamWriter.

### Usage

    getRefData(object)

### Arguments

`object` | `bamReader`. The reader must be opened (otherwise an error is thrown).

### Details

`getRefData` returns a `data.frame` with three columns (ID, SN, LN). ID is the (0-based index which must be given when a `bamRange` is extracted. SN is the name of the sequence (e.g. chr1 for UCSC). LN is the length of the reference sequence. `getRefCount` returns the number of reference sequences. `getRefCoords` returns a vector of coordinates which can be used to extract all stored aligns for this sequence from the `bamReader` into a `bamRange` object.

### Author(s)

Wolfgang Kaisers

### Examples

    bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
    reader<-bamReader(bam,idx=TRUE)
    getRefData(reader)
    getRefCount(reader)
    getRefId(reader, "chr1")
    coords<-getRefCoords(reader, "chr1")
    rg<-bamRange(reader,coords)
    bamClose(reader)

[Package rbamtools version 2.16.17 Index]