parse_hmp_qiime

(<code>character</code> of length 1) A file path or URL to the OTU table.

otu_file

(<code>character</code> of length 1) A file path or URL to the sample mapping file.

mapping_file

(<code>numeric</code> of length 1) Do not return rows less abundance. This can make the output object much smaller.

min_abundance

(<code>numeric</code> of length 1) Only parse some number of OTUs. Useful for making small datasets for testing.

max_otus


NOTE: Not extensivley tested
Parses the results of the Human Microbiome Project QIIME analysis of the 16S metagenomic data.
This is mostly a wrapper for <code><a rd-options="" href="/link/extract_taxonomy?package=metacoder&version=0.1.2" data-mini-rdoc="metacoder::extract_taxonomy">extract_taxonomy</a></code>.


A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).

Zachary Foster

metacoder

Tools for Parsing, Manipulating, and Graphing Hierarchical Data

parse_hmp_qiime function


NOTE: Not extensivley tested
Parses the results of the Human Microbiome Project QIIME analysis of the 16S metagenomic data.
This is mostly a wrapper for <code><a rd-options='' href='extract_taxonomy'>extract_taxonomy</a></code>.


parse_hmp_qiime: Parse HMP QIIME results

Description

Usage

Arguments

Value