metacoder (version 0.3.7)

ambiguous_patterns: Get patterns for ambiguous taxa

Description

This function stores the regex patterns for ambiguous taxa.

Usage

ambiguous_patterns(
  unknown = TRUE,
  uncultured = TRUE,
  case_variations = FALSE,
  whole_match = FALSE,
  name_regex = "."
)

Arguments

unknown

If TRUE, Remove taxa with names the suggest they are placeholders for unknown taxa (e.g. "unknown ...").

uncultured

If TRUE, Remove taxa with names the suggest they are assigned to uncultured organisms (e.g. "uncultured ...").

case_variations

If TRUE, include variations of letter case.

whole_match

If TRUE, add "^" to front and "$" to the back of each pattern to indicate they are to match whole words.

name_regex

The regex code to match a valid character in a taxon name. For example, "[a-z]" would mean taxon names can only be lower case letters.