| parse_qiime_biom {metacoder} | R Documentation |
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")
Arguments
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 |
('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:
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()