BIOMsubset: Take part of (subset) BIOM data
In MG-RAST/matR: Metagenomics Analysis Tools

Description Usage Arguments Details Value Author(s) See Also Examples

Take part of (subset) an object of class biom by removing rows, columns, or both.

1 2	## S3 method for class 'biom' x[i, j, ...]

`x`	an object (`biom`)
`i`	row index (`integer`, `character`, or `logical`)
`j`	column index (`integer`, `character`, or `logical`)
`...`	unused

Complete technical documentation is forthcoming. For the current preliminary release, please refer to the examples provided.

A biom object, the specified subset of x.

Daniel T. Braithwaite

BIOM.utils::biom, BIOM.utils::dim.biom

####  explicit subsetting
xx3 [ , 1:8]
xx4 [c ("Bacteria", "Eukaryota"), c ("mgm4575333.3", "mgm4575334.3", "mgm4575335.3")]

####  keep only metagenomes from one biome
xx3 [ , columns (xx3, "biome") == "Tundra biome"]

####  keep only rows matching a search term
xx1 [grepl ("Protein secretion system", rownames(xx1)), ]