biom_raw_data: Extract raw data from a BIOM object.
Description
This function extracts the raw data from a BIOM object, using the correct
row and column names in the result.
Usage
biom_raw_data(b)
Arguments
b
A BIOM object.
Value
For sparse biom objects, returns a 3-column data frame of row names,
column names, and the data value. The first column is named using the
first word in the BIOM object's type attribute (e.g. "OTU" for OTU
tables). The second and third columns are named "SampleID" and "value",
respectively. For dense biom objects, returns a matrix.
Details
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.