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biom (version 0.3.9)

An interface package (beta) for the BIOM file format.

Description

This is an R package for interfacing with the BIOM format. Currently in beta form, this package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

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Install

install.packages('biom')

Monthly Downloads

8

Version

0.3.9

License

GPL-2 | file LICENSE

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Repository

https://github.com/biom-format/biom-format

Homepage

http://biom-format.org/

Maintainer

Paul McMurdie

Last Published

May 22nd, 2013

Functions in biom (0.3.9)

The biom format data class.

sample_metadata

Access meta data from biom-class.

Access main data observation matrix data from biom-class.

Write a biom-format file, returning a biom-class.

Method extensions to ncol for biom-class objects.

Build and return an instance of the biom-class.

The matrix dimensions of a biom-class object.

matrix_element_type

Access class of data in the matrix elements of a biom-class object

Read a biom-format file, returning a biom-class.

observation_metadata

Access observation (row) meta data from biom-class.

Method extensions to show for biom objects.

Method extensions to nrow for biom-class objects.

Method extensions to rownames for biom-class objects.

Extract the header from a biom-class object as a list.

Method extensions to colnames for biom-class objects.

This is an R package for interfacing with the biom format.