Convert the ASV table and taxonomy table returned by dada2 into a taxmap object. An example of the input format can be found by following the dada2 tutorial here: shttps://benjjneb.github.io/dada2/tutorial.html
parse_dada2(seq_table, tax_table, class_key = "taxon_name",
class_regex = "(.*)", include_match = TRUE)
The ASV abundance matrix, with rows as samples and columns as ASV ids or sequences
The table with taxonomic classifications for ASVs, with ASVs in rows and taxonomic ranks as columns.
(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.
(character
of length 1) A regular expression with capturing groups
indicating the locations of data for each taxon in the class
term in the key
argument. The
identity of the information must be specified using the class_key
argument. The class_sep
option can be used to split the classification into data for each taxon before matching. If
class_sep
is NULL
, each match of class_regex
defines a taxon in the classification.
(logical
of length 1) If TRUE
, include the part of the input matched by
class_regex
in the output object.
Other parsers: parse_edge_list
,
parse_greengenes
,
parse_mothur_tax_summary
,
parse_mothur_taxonomy
,
parse_newick
, parse_phyloseq
,
parse_phylo
,
parse_qiime_biom
, parse_rdp
,
parse_silva_fasta
,
parse_ubiome
,
parse_unite_general