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