taxonomy: Assign taxonomy to nucleotide sequences

In brendanf/phylotax: Refine taxonomic assignment of environmental sequences using a taxonomic tree

Description

This method uses a common interface to call primary taxonomic assignment algorithms (i.e., those which assign taxonomy based on a taxonomically classified reference sequence database, but not based on the results of other algorithms) from other R packages or external programs.

Usage

taxonomy(seq, reference, method, min_confidence = 50, multithread = FALSE, ...)

taxonomy_dada2(
  seq,
  reference,
  multithread = FALSE,
  min_confidence,
  tryRC = FALSE,
  outputBootstraps = TRUE,
  verbose = TRUE,
  ...
)

taxonomy_sintax(
  seq,
  reference,
  min_confidence = NULL,
  multithread = FALSE,
  exec = NULL,
  ...
)

taxonomy_idtaxa(
  seq,
  reference,
  multithread = FALSE,
  strand = "top",
  min_confidence = 40,
  ...
)

Arguments

seq	('character“ vector or something that can be coerced to one, or a matrix with sequences as the column names ) Sequences to assign taxonomy
reference	('character“ string giving a path to a file or the result from DECIPHER::LearnTaxa()/train_idtaxa()) An appropriately formatted reference database (see Details).
method	('character“ string) taxonomy assignment method. Currently accepted values are "dada2", "sintax", and "idtaxa".
min_confidence	('integer“ between 0 and 100) The minimum confidence to report results.
multithread	(integer scalar) the number of processors to use for assignment.
...	additional arguments for methods
tryRC	(logical scalar) passed on to dada2::assignTaxonomy()
outputBootstraps	(logical scalar) passed on to dada2::assignTaxonomy()
verbose	(logical scalar) passed on to dada2::assignTaxonomy()
exec	(character string) name of the executable to use for SINTAX search. The default is "vsearch", but "usearch" should also work. In either case, the executable should be installed and on the system path.
strand	(character string) passed on to DECIPHER::IdTaxa()

Value

raw results of the taxonomy assignment, of various types depending on method.

Return types

• taxonomy_dada2 and taxonomy(..., method = "dada2") return a list with elements "tax" and "boot", as dada2::assignTaxonomy.

• taxonomy_sintax and taxonomy(..., method = "sintax") return a data.frame with columns "label", "hit", "strand", and, if min_confidence is not given, "c12n" (short for "classification").

• taxonomy_idtaxa and taxonomy(..., method = "idtaxa") gives an S4 object of classes "Taxa" and "Train". Any of these can be passed to taxtable to get a uniform format suitable for use in phylotax.

brendanf/phylotax documentation built on March 3, 2021, 2:21 p.m.