check_tax_uniqueness: Check taxonomy uniqueness.

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Check taxonomy uniqueness.

Description

This function checks for the duplicate taxonomy names that can occur in different groups (e.g., the same genus names in different families).

Usage

check_tax_uniqueness(x, col = "k", return_all = F, dropNA = T)

Arguments

x	Data frame with taxonomy (columns = taxonomy ranks, rows = species)
col	Column name (taxonomy rank) that should be checked for uniqueness
return_all	Logical; default, FALSE - only non-unique values will be returned
dropNA	Logical; default, TRUE - missing values within the selected column ('col') will be removed

Value

Data frame with counts of taxon occurence (by default, only non-unique values will be shown).

Examples

datt <- data.frame(
  Kingdom = rep(LETTERS[1:2], each = 6),
  Phylum = rep(LETTERS[3:6], each = 3),
  Class = rep(letters[1:6], times = 2),
  stringsAsFactors = F
  )

check_tax_uniqueness(datt, col = "Phylum") # All ranks of Phylum are unique
check_tax_uniqueness(datt, col = "Class")  # Classes are duplicated

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.