build_kmer_database: Build kmer database

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

Build kmer database

Description

Build kmer database for classifying 16S rRNA and other gene sequences to a genus when a kmer size is provided.

Usage

build_kmer_database(classification_database, kmer_size = 8)

Arguments

classification_database	A classification_database object, which is a list containing the fields seq_taxonomy_data and reference_data. These are both data.frame objects. The package includes rdp_trainset9 and rdp_trainset9_pds. Other databases can be obtained from phylotyprrefdata or by using create_database()
kmer_size	An integer indicating the length of the nucleotide word to base our classification on (default = 8)

Value

A list object containing the genus level conditional probability (conditional_prob) of seeing each kmer in a given genus as well as the genus names (genera)

References

Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 Aug;73(16):5261-7. \Sexpr[results=rd]{tools:::Rd_expr_doi("doi:10.1128/AEM.00062-07")} PMID: 17586664; PMCID: PMC1950982.

Examples

kmer_size <- 8

## Not run: 
# Function takes >5 s to run on this database
build_kmer_database(rdp_trainset9_pds, kmer_size)

## End(Not run)

phylotypr documentation built on Oct. 22, 2026, 5:21 p.m.