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.
parse_qiime_biom(file, class_regex = "(.*)", class_key = "taxon_name")
A taxmap object
(character
of length 1) The file path to the input file.
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.
(`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.
This function was inspired by the tutorial created by Geoffrey Zahn at http://geoffreyzahn.com/getting-your-otu-table-into-r/.
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()