BIOMsubset: Take part of (subset) BIOM data

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

Description

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

Usage

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

Arguments

x

an object (biom)

i

row index (integer, character, or logical)

j

column index (integer, character, or logical)

...

unused

Details

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

Value

A biom object, the specified subset of x.

Author(s)

Daniel T. Braithwaite

See Also

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

Examples

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####  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)), ]

matR documentation built on May 2, 2019, 6:53 a.m.