parse_hmp_qiime: Parse HMP QIIME results

Description Usage Arguments Value

View source: R/extract_taxonomy--wrappers.R

Description

NOTE: Not extensively tested Parses the results of the Human Microbiome Project QIIME analysis of the 16S metagenomic data. This is mostly a wrapper for extract_taxonomy.

Usage

1
parse_hmp_qiime(otu_file, mapping_file, min_abundance = 1, max_otus = -1)

Arguments

otu_file

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

mapping_file

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

min_abundance

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

max_otus

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

Value

A taxmap object


metacoder documentation built on May 30, 2017, 3:11 a.m.