filter_taxonomy: Filter taxonomy

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

Filter taxonomy

Description

The filter_taxonomy() function will filter a consensus taxonomy to remove any taxonomic levels where the confidence score is below a min_confidence level

Usage

filter_taxonomy(consensus, min_confidence = 80)

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
min_confidence	A double value between 0 and 100 (default = 80). The minimum percentage of bootstrap replicates that had the same classification. Any confidence score below this value will have the corresponding taxonomy removed

Value

A list object containing two equally sized vectors that are filtered to remove low confidence taxonomies. One vector, taxonomy, contains the taxonomy at each taxonomic level and the other vector, confidence contains the confidence score for that taxonomy. There will be no taxonomies or confidence scores below min_confidence

Examples

oscillospiraceae <- list(
  taxonomy = c(
    "Bacteria", "Bacillota", "Clostridia",
    "Eubacteriales", "Oscillospiraceae",
    "Flintibacter"
  ),
  confidence = c(100, 100, 99, 99, 98, 58)
)

filter_taxonomy(oscillospiraceae, min_confidence = 80)

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