parse_dada2: Convert the output of dada2 to a taxmap object

In grunwaldlab/metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Convert the output of dada2 to a taxmap object

Description

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

Usage

parse_dada2(
  seq_table,
  tax_table,
  class_key = "taxon_name",
  class_regex = "(.*)",
  include_match = TRUE
)

Arguments

seq_table	The ASV abundance matrix, with rows as samples and columns as ASV ids or sequences
tax_table	The table with taxonomic classifications for ASVs, with ASVs in rows and taxonomic ranks as columns.
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.
class_regex	('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.
include_match	('logical' of length 1) If 'TRUE', include the part of the input matched by 'class_regex' in the output object.

Value

taxmap

See Also

Other parsers: extract_tax_data(), lookup_tax_data(), parse_edge_list(), parse_greengenes(), parse_mothur_tax_summary(), parse_mothur_taxonomy(), parse_newick(), parse_phylo(), parse_phyloseq(), parse_qiime_biom(), parse_rdp(), parse_silva_fasta(), parse_tax_data(), parse_ubiome(), parse_unite_general()

grunwaldlab/metacoder documentation built on Feb. 22, 2024, 3:47 a.m.