parse_qiime_biom

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Parse a BIOM output from QIIME

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: 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_ubiome, parse_unite_general

Aliases
  • parse_qiime_biom
Documentation reproduced from package metacoder, version 0.3.3, License: GPL-2 | GPL-3

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