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metacoder (version 0.3.7)

parse_qiime_biom: 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")

Value

A taxmap object

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/.

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_phylo(), parse_phyloseq(), parse_rdp(), parse_silva_fasta(), parse_tax_data(), parse_ubiome(), parse_unite_general()