qiimer (version 0.9.4)

read_qiime_otu_table: Parse a QIIME OTU table file in "calssic" format.

Description

Parse a QIIME OTU table file in "calssic" format.

Usage

read_qiime_otu_table(filepath, commented = TRUE, metadata = TRUE)

Arguments

filepath

Path to OTU table file.

commented

TRUE if the header line is preceeded by an additional comment line, otherwise FALSE. This is usually the case for OTU tables generated with QIIME, so we default to TRUE.

metadata

TRUE if the OTU table contains a metadata column, otherwise FALSE. The metadata column usually contains taxonomic assignments, and must be located on the right-hand side of the table.

Value

A list with four attributes: sample_ids, otu_ids, counts, and metadata, a data structure similar to that returned by the python function `qiime.parse.parse_otu_table`. The sample_ids, otu_ids, and metadata attributes are character vectors. The counts attribute is a matrix with one column per sample_id and one row per otu_id.