parse_dada2

0th

Percentile

Convert the output of dada2 to a taxmap object

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: 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

Aliases
  • parse_dada2
Documentation reproduced from package metacoder, version 0.3.3, License: GPL-2 | GPL-3

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