dada2 (version 1.0.3)

assignTaxonomy: Classifies sequences against reference training dataset.

Description

assignTaxonomy implements the RDP classifier algorithm in Wang 2007 with kmer size 8 and 100 bootstrap replicates.

Usage

assignTaxonomy(seqs, refFasta, minBoot = 50, verbose = FALSE)

Arguments

seqs

(Required). A character vector of the sequences to be assigned, or an object coercible by getUniques.

refFasta

(Required). The path to the reference fasta file, or an R connection Can be compresssed. This reference fasta file should be formatted so that the id lines correspond to the taxonomy (or classification) of the associated sequence, and each taxonomic level is separated by a semicolon. Eg.

>Kingom;Phylum;Class;Order;Family;Genus; ACGAATGTGAAGTAA......

minBoot

(Optional). Default 50. The minimum bootstrap confidence for assigning a taxonomic level.

verbose

(Optional). Default FALSE. If TRUE, print status to standard output.

Value

A character matrix of assigned taxonomies exceeding the minBoot level of bootstrapping confidence. Rows correspond to the provided sequences, columns to the taxonomic levels. NA indicates that the sequence was not consistently classified at that level at the minBoot threshhold.

Examples

## Not run: 
#  taxa <- assignTaxonomy(dadaF, "gg_13_8_train_set_97.fa.gz")
#  taxa <- assignTaxonomy(dadaF, "rdp_train_set_14.fa.gz", minBoot=80)
# ## End(Not run)