tidy_taxonomy: Clean up the taxonomic table to make taxonomic assignments...

In microeco: Microbial Community Ecology Data Analysis

Clean up the taxonomic table to make taxonomic assignments consistent.

Description

Clean up the taxonomic table to make taxonomic assignments consistent.

Usage

tidy_taxonomy(
  taxonomy_table,
  column = "all",
  pattern = c(".*unassigned.*", ".*uncultur.*", ".*unknown.*", ".*unidentif.*",
    ".*unclassified.*", ".*No blast hit.*", ".*Incertae.sedis.*"),
  replacement = "",
  add_prefix = TRUE,
  ignore.case = TRUE,
  na_fill = ""
)

Arguments

taxonomy_table	a data.frame with taxonomic information (rows are features; columns are taxonomic levels); or a microtable object with tax_table in it.
column	default "all"; "all" or a number; 'all' represents cleaning up all the columns; a number represents cleaning up this specific column.
pattern	default c(".*unassigned.*", ".*uncultur.*", ".*unknown.*", ".*unidentif.*", ".*unclassified.*", ".*No blast hit.*", ".*Incertae.sedis.*"); the characters (regular expressions) to be removed or replaced; removed when parameter replacement = "", replaced when parameter replacement has something; Note that the capital and small letters are not distinguished when ignore.case = TRUE.
replacement	default ""; the characters used to replace the character in pattern parameter. Note that after the replacement is completed, if the parameter add_prefix is set to TRUE, a prefix (e.g., "g__") based on the taxonomic names will be added to the result.
add_prefix	default TRUE; whether add the taxonomic prefix (e.g., "g__" for Genus level) after the replacement and other operations.
ignore.case	default TRUE; if FALSE, the pattern matching is case sensitive and if TRUE, case is ignored during matching.
na_fill	default ""; used to replace NA.

Value

data.frame or microtable object depending on the input data format.

Examples

data("taxonomy_table_16S")
tidy_taxonomy(taxonomy_table_16S)

microeco documentation built on Oct. 20, 2026, 9:06 a.m.