R: Extract raw data from a BIOM object.

biom_raw_data {qiimer} | R Documentation

## 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.

### 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.

### 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.

### Examples

    data(relmbeta_biom)
    head(biom_raw_data(relmbeta_biom))

[Package qiimer version 0.9.4 Index]