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