biom_raw_data: Extract raw data from a BIOM object.

In kylebittinger/qiimer: Work with QIIME Output Files in R

Description

WARNING: This function has been removed. Previous versions of this function did not give the correct result under some circumstances. If you have used this function previously, please check your work by converting the BIOM file to classic tab-separated values format and importing with the function read_qiime_otu_table().

Usage

biom_raw_data(b)

Arguments

b	A BIOM object.

Details

This function extracts the raw data from a BIOM object, using the correct row and column names in the result.

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))

kylebittinger/qiimer documentation built on May 20, 2019, 7:30 p.m.