R: Reading, writing and manipulating BAM-file format.

rbamtools-package {rbamtools} | R Documentation

## Reading, writing and manipulating BAM-file format.

### Description

BAM is Binary (Sequence) Alignment/Map format. Many sequence alignment products which align second generation sequence reads to a genomic reference (such as the human genome) use BAM-file format as output. Analysis of results of a sequence alignment requires reading and interpreting BAM-files and sometimes manipulating BAM-files. The rbamtools package provides a R-interface to the samtools C-library by Heng Li.

### Details

Package: | rbamtools
Type: | Package
Version: | 2.0
Date: | 2012-02-03
License: | Artistic 2.0 + MIT License (see LICENSE in src/samtools subdirectory)
LazyLoad: | yes
Depends: | methods

The package is organized in S4 classes. Four classes represent the data and organize the defined functionality:

bamReader | Reading aligns from a BAM-file
bamAlign | Single BAM alignment (including Data accessor functions)
bamRange | (Linked-) List container for BAM alignments
bamWriter | Writing alings to a BAM-file
gapList | (Linked-) List container for alignment gaps.

### Author(s)

Wolfgang Kaisers Maintainer: Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>

### References

`The SAM Format Specification (v1.4-r985). The SAM Format Specification Working Group. September 7, 2011.` `Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9.`

### Examples

    bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
    idx <- system.file("extdata", "accepted_hits.bam.bai", package="rbamtools")
    #
    reader<-bamReader(bam)
    isOpen(reader)
    #
    align<-getNextAlign(reader)
    #
    loadIndex(reader,idx)
    indexInitialized(reader)
    #
    coords<-as.integer(c(0,0,249250621))
    range<-bamRange(reader,coords)
    align<-getNextAlign(range)
    #
    bamClose(reader)

[Package rbamtools version 2.16.17 Index]