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Assign taxonomy with dada2 using 2 steps assignTaxonomy and assignSpecies

Source: R/dada_phyloseq.R
assign_dada2.Rd

lifecycle-experimental

Mainly a wrapper of dada2::assignTaxonomy() and dada2::assignSpecies()

Usage

assign_dada2(
  physeq = NULL,
  ref_fasta = NULL,
  seq2search = NULL,
  min_bootstrap = 0.5,
  tryRC = FALSE,
  taxa_ranks = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species",
    "taxId"),
  use_assignSpecies = TRUE,
  trunc_absent_ranks = FALSE,
  nproc = 1,
  suffix = "",
  verbose = TRUE,
  seq_at_one_time = 2000,
  allowMultiple = FALSE,
  from_sintax = FALSE
)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

ref_fasta

(required) A link to a database in fasta.

A DNAStringSet object of sequences to search for. Replace the physeq object.

min_bootstrap

(Float [0:1], default 0.5), See dada2::assignTaxonomy()

tryRC

See dada2::assignTaxonomy()

taxa_ranks

(vector of character) names for the column of the taxonomy

use_assignSpecies

(logical, default TRUE) Do the Species rank is obtained using dada2::assignSpecies() ?

trunc_absent_ranks

(logical, default FALSE) Do ranks present in taxa_ranks but not present in the database are removed ?

nproc

(Float [0:1], default 0.5)

suffix

(character) The suffix to name the new columns. Default to "_idtaxa".

verbose

(logical). If TRUE, print additional information.

seq_at_one_time

How many sequences are treated at one time. See param n in dada2::assignSpecies()

allowMultiple

(logical, default FALSE). Unchanged from dada2::assignSpecies(). Defines the behavior when multiple exact matches against different species are returned. By default only unambiguous identifications are return. If TRUE, a concatenated string of all exactly matched species is returned. If an integer is provided, multiple identifications up to that many are returned as a concatenated string.

from_sintax

(logical, default FALSE). Set to TRUE if the ref_fasta database is in sintax format. See assign_sintax() for more information about the sintax format.

Value

Either a an object of class phyloseq (if physeq is not NULL), or a taxonomic table if seq2search is used in place of physeq

Examples

if (FALSE) { # \dontrun{
data_fungi_mini2 <- assign_dada2(data_fungi_mini,
  ref_fasta = system.file("extdata", "mini_UNITE_fungi.fasta.gz",
    package = "MiscMetabar"
  ), suffix = "_dada2",
  from_sintax = TRUE
)
} # }