pbh5-package: Interact with Pacific Biosciences HDF5 Files

Description Details Author(s) See Also Examples

Description

The pbh5 package provides an interface to the various HDF5 files produced by Pacific Biosciences. These files can be used to access unique features of "PacBio" data not readily available in standard formats such as SAM/BAM and FASTA/FASTQ.

The package is structured around a set of hdf5 file formats and the classes used to represent them. The hdf5 format is a robust infrastructure for the construction of binary file formats. More information can be found at: www.hdfgroup.org. Roughly, it is a filesystem for your data. At the R level, the pbh5 package depends on the h5r package which is an open-source package located on r-forge. This package provides a generic read/write interface to hdf5 files.

The core classes defined in the pbh5 package are: PacBioCmpH5 (pronounced comp h5), PacBioBasH5 (pronounced base h5), PacBioPlsH5 (pronounced pulse h5). The pbh5 package also supports two other formats which will be encountered less frequently, if at all: PacBioTrcH5 (pronounced trace h5) and PacBioAlnH5 (pronounced align h5).

All classes should be considered read-only in the sense that any modification of the underlying properties will have undefined consequences. Additionally, access to the data stored in the classes should proceed (almost) entirely through functions and methods defined in the package. To the extent possible, objects are returned as simple R objects.

Bugs should be reported to: <jbullard@pacificbiosciences.com>.

Details

Package: pbh5
Version: 1.0
Date: 2010-07-02
License: BSD
LazyLoad: yes
Depends: methods, h5r

Author(s)

Maintainer: <jbullard@pacificbiosciences.com>

See Also

The h5r package.

Examples

1
 ls('package:pbh5')

PacificBiosciences/R-pbh5 documentation built on May 7, 2019, 11:54 p.m.