parse_qiime_biom: Parse a BIOM output from QIIME

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Parse a BIOM output from QIIME

Description

Parses a file in BIOM format from QIIME into a taxmap object. This also seems to work with files from MEGAN. I have not tested if it works with other BIOM files.

Usage

parse_qiime_biom(file, class_regex = "(.*)", class_key = "taxon_name")

Arguments

file	(character of length 1) The file path to the input file.
class_regex	A regular expression used to parse data in the taxon names. There must be a capture group (a pair of parentheses) for each item in class_key. See parse_tax_data for examples of how this works.
class_key	('character' of length 1) The identity of the capturing groups defined using 'class_regex'. The length of 'class_key' must be equal to the number of capturing groups specified in 'class_regex'. Any names added to the terms will be used as column names in the output. At least one '"taxon_name"' must be specified. Only '"info"' can be used multiple times. Each term must be one of those described below: * 'taxon_name': The name of a taxon. Not necessarily unique, but are interpretable by a particular 'database'. Requires an internet connection. * 'taxon_rank': The rank of the taxon. This will be used to add rank info into the output object that can be accessed by 'out$taxon_ranks()'. * 'info': Arbitrary taxon info you want included in the output. Can be used more than once.

Details

This function was inspired by the tutorial created by Geoffrey Zahn at http://geoffreyzahn.com/getting-your-otu-table-into-r/.

Value

A taxmap object

See Also

Other parsers: extract_tax_data(), lookup_tax_data(), parse_dada2(), parse_edge_list(), parse_greengenes(), parse_mothur_tax_summary(), parse_mothur_taxonomy(), parse_newick(), parse_phyloseq(), parse_phylo(), parse_rdp(), parse_silva_fasta(), parse_tax_data(), parse_ubiome(), parse_unite_general()

metacoder documentation built on April 4, 2023, 9:08 a.m.