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
.
parse_hmp_qiime(otu_file, mapping_file, min_abundance = 1, max_otus = -1)
(character
of length 1) A file path or URL to the OTU table.
(character
of length 1) A file path or URL to the sample mapping file.
(numeric
of length 1) Do not return rows less abundance. This can make the output object much smaller.
(numeric
of length 1) Only parse some number of OTUs. Useful for making small datasets for testing.
A taxmap
object