create_database: Build custom database object for use with phylotypr

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

Build custom database object for use with phylotypr

Description

The create_database() function builds a classification_database object that can be used to generate the kmer database for downstream use in classify_sequences(). This function is only necessary if you are building your own database or modifying one of the existing databases provided in {phylotypr} or {phylotyprrefdata}.

Usage

create_database(sequence_name, sequence, taxonomy, reference_data = NULL)

Arguments

sequence_name	A character vector of identifiers for each sequence in the database. Should have the same number of values as found in the sequence and taxonomy vectors.
sequence	A character vector of the sequences that are included in the database. Should have the same number of values as found in the sequence_name and taxonomy vectors.
taxonomy	A character vector of taxonomy data for each sequence in the database. Should have the same number of values as found in the sequence_name and sequence vectors. The format of each value should be with each taxonomic level separated by a semicolon. Ideally each value in taxonomy will have the same number of levels.
reference_data	single row data frame object that has columns vendor, name, version, usage, notes, method_url, documentation_url, and citation. This is supplied with databases obtained from phylotyprrefdata. This information is only used if user supplied sequences are supplied as a strollur object.

Value

A classification_database object, which is a list containing the fields seq_taxonomy_data and reference_data. These are both data.frame objects.

Examples

sequence_name <- c("seq_a", "seq_b", "seq_c")
sequence <- c("AAAATCGAGTA", "ATGCGCTCCCC", "ATGCGCTCCCC")
genera <- c("A;b;C;d", "A;b;C;e", "A;b;C;e")

create_database(
  sequence_name = sequence_name,
  sequence = sequence,
  taxonomy = genera
)

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