R: Import and Export BIOM Objects

BIOM Import and Export {KbaseKit}

R Documentation

Import and Export BIOM Objects

Description

Easy import and export of objects in the JSON-based Biological Observation Matrix (BIOM) format. Imports lightly encapsulate the BIOM object's numerical data and metadata. Exports write a valid BIOM object.

Usage

fromBIOM(file, keepSparse = TRUE)
toBIOM(obj, type, ID = NULL, comment = "", asSparse = TRUE, toFile = NULL)

Arguments

`obj`	`matrix`, `sparseMatrix`, or `data.frame`
`type`	Character: one of `"OTU table"`, `"Pathway table"`, `"Function table"`,`"Ortholog table"`,`"Gene table"`,`"Metabolite table"`,`"Taxon table"`
`ID`	Optional, character
`comment`	Optional, character
`asSparse`	Logical: whether to create a `\"sparse\"` or `\"dense\"` `BIOM` object
`toFile`	Destination file
`file`	Character: JSON content, name of source file, or URL
`keepSparse`	Logical: if `TRUE` and the `BIOM` object is sparse, a `sparseMatrix` will be created, otherwise an ordinary `matrix`

Details

The object created by fromBIOM is of class kb, which encapsulates metadata but can be used as a matrix (or sparseMatrix, as the case may be). toBIOM writes a correct BIOM object and returns the filename, or if toFile is NULL, returns the object itself as text.

Author(s)

Daniel Braithwaite

References

http://www.biom-format.org/