classify_sequences: Classify a vector of 16S rRNA gene sequence fragments

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

Classify a vector of 16S rRNA gene sequence fragments

Description

The classify_sequences() function implements the Wang et al. naive Bayesian classification algorithm for 16S rRNA gene sequence.

Usage

classify_sequences(
  data = NULL,
  sequence,
  sequence_name = as.character(seq_along(sequence)),
  database,
  kmer_size = 8,
  num_bootstraps = 100,
  min_confidence = 80,
  seed = 1,
  num_processors = parallelly::availableCores()
)

Arguments

data	A data frame containing a column of sequence_name and sequence. If provided column names need to be provided to sequence_name and sequence.
sequence	A vector of character objects representing DNA sequence that need to be classified. If data is provided then only the name of the column containing sequence needs to be provided, quotation marks are optional. This argument can be ignored when using a {strollur} object
sequence_name	A vector of character objects containing the sequence name that need to be classified. Optional. Defaults to the position of the sequence in the vector of sequence. If data is provided then only the name of the column containing the sequence name needs to be provided, quotation marks are optional. This argument can be ignored when using a {strollur} object
database	A kmer database generated using build_kmer_database
kmer_size	An integer value (default of 8) indicating the size of kmers to use for classifying sequence. Higher values use more RAM with potentially more specificity Lower values use less RAM with potentially less specificity. Benchmarking has found that the default of 8 provides the best specificity with the lowest possible memory requirement and fastest execution time.
num_bootstraps	An integer value (default of 100). The value of num_bootstraps is the number of randomizations to perform where 1/kmer_size of all kmers are sampled (without replacement) from unknown_sequence. Higher values will provide greater precision on the confidence score.
min_confidence	An integer value (default of 80). The value of min_confidence represents the minimum number of bootstraps that must have a classification that agree with each other.
seed	An integer value (default of 1). The value of seed sets the seed for the random number generator.
num_processors	An integer value. The value of num_processors indicates the number of desired processors. Defaults to all available cores using parallelly::availableCores()

Value

A data frame object with three columns: the sequence name (sequence_name), the taxonomic assignment for each level (taxonomy), and the confidence associated with that classification level (confidence). The value in confidence represents the percentage of num_bootstraps that the classifier gave the same classification at that level.

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 <- 3
reference_names <- c("seq_1", "seq_2", "seq_3")
reference_sequences <- c("ATGCGCTA", "ATGCGCTC", "ATGCGCTC")
reference_genera <- c("A", "B", "B")
reference <- create_database(reference_names, reference_sequences, reference_genera)

db <- build_kmer_database(reference, kmer_size)

unknown_sequence <- c("ATGCGCTC", "ATGCGCTC", "ATGCGCTC")
unknown_id <- c("seq_1", "seq_2", "seq_3")

classify_sequences(
  sequence = unknown_sequence,
  database = db,
  kmer_size = kmer_size,
  seed = 1,
  num_processors = 1
)

classify_sequences(
  sequence = unknown_sequence,
  sequence_name = unknown_id,
  database = db,
  kmer_size = kmer_size
)

classify_sequences(
  sequence = "ATGATCGAGTC",
  database = db,
  kmer_size = kmer_size,
  min_confidence = 95
)

sequence_df <- data.frame(
  seq_names = unknown_id,
  seqs = unknown_sequence
)

classify_sequences(sequence_df,
  sequence_name = seq_names, sequence = seqs,
  database = db, kmer_size = 3
)

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