parse_hmp_qiime

0th

Percentile

Parse HMP QIIME results

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
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

Aliases
  • parse_hmp_qiime
Documentation reproduced from package metacoder, version 0.1.3, License: GPL-2 | GPL-3

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