biom_taxonomy: Extract taxonomy info from a biom object.
Description
For BIOM objects representing OTU tables, this function will extract the
taxonomy for each OTU. The taxonomy info is typically stored in an
attribute of the row metadata named "taxonomy".
Usage
biom_taxonomy(b, attr = "taxonomy")
Arguments
b
A BIOM object.
attr
The metadata attribute under which the taxonomy information
can be found for each row item in the biom file.
Value
A list of character vectors, one per row.
Details
This function may be used more generally to extract metadata from rows in a
BIOM object. The attr argument may be adjusted to match the desired
attribute name. If the metadata has a nested structure, a character vector
may be supplied to the attr argument.
The BIOM object can be any list-like representation of the JSON
source code in a BIOM-format file produced by QIIME. There are several
options for creating BIOM objects from QIIME output files. The official
library for BIOM files, biom, can create compatible objects via the
read_biom function. Alternately, the fromJSON function from
either RJSONIO or rjson may be used.