print_taxonomy: Print taxonomy for an unknown sequence

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

Print taxonomy for an unknown sequence

Description

The print_taxonomy() will output the consensus taxonomy for an unknown sequence with confidence scores for each taxonomic level and each taxonomic level separated by semi-colons

Usage

print_taxonomy(consensus, n_levels = 6)

Arguments

consensus	A list object that contains two slots each with an equal sized vector. The taxonomy vector contains the classification at each taxonomic level and the confidence vector contains the percentage of bootstraps that had the specified classification
n_levels	An integer indicating the number of taxonomic levels to expect. If the number of observed levels is less than this value, then missing levels will have "_unclassified" to the end of the last named classification

Value

A character string indicating the classification at each taxonomic level with the corresponding confidence in parentheses. Each taxonomic level is separated by a semi-colon

Examples

oscillospiraceae <- list(
  taxonomy = c(
    "Bacteria", "Bacillota", "Clostridia",
    "Eubacteriales", "Oscillospiraceae"
  ),
  confidence = c(100, 100, 99, 99, 98)
)

print_taxonomy(oscillospiraceae, n_levels = 6)

phylotypr documentation built on April 3, 2025, 5:51 p.m.