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

read_qiime_otu_table {qiimer} | R Documentation

## 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.

[Package qiimer version 0.9.4 Index]