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Count unwanted values in a taxonomy table

Source: R/summarize.R
count_unwanted_tax.Rd

Scans a taxonomy table for common problematic values such as NA-like strings, placeholder labels ("unclassified", "unknown", etc.), and empty QIIME-style rank prefixes. The input can be a phyloseq object or a FASTA reference database file.

Returns a tibble summarising, for each pattern found, how many matches occur in each taxonomic rank.

Usage

count_unwanted_tax(
  x,
  patterns = unwanted_tax_patterns_default(),
  tax_format = "auto"
)

Arguments

x

Either:

  • a character string giving the path to a FASTA file (plain or gzip), or

  • a phyloseq object with a taxonomy table.

patterns

(Character vector) Regular expressions to search for. When MiscMetabar is installed, defaults to MiscMetabar::unwanted_tax_patterns; otherwise falls back to a built-in copy of the same patterns. See Details.

tax_format

(Character) Taxonomy format of the FASTA file. One of "unite", "sintax", "greengenes2", "pr2", or "auto". Only used when x is a file path. If "auto" (default), the format is detected with detect_tax_format(). Ignored when x is a phyloseq object.

Value

A tibble with columns:

pattern

The regular expression that matched.

description

A human-readable label for the pattern.

rank

The taxonomic rank (column name) where matches were found.

n_matches

Number of values matching the pattern in that rank.

example_values

Up to 3 unique matching values (comma-separated).

Rows with zero matches are omitted.

Details

The default patterns are:

"^[Nn][Aa][Nn]?$"

NaN, nan, NA, na

"^[Nn]/[Aa]$"

N/A, n/a

"^[Nn]one$"

None, none

"^$"

empty string

"^\\s+$"

whitespace only

"[Uu]nclassified"

unclassified, Unclassified, xxx_unclassified

"[Uu]nknown"

unknown, Unknown, xxx_unknown

"[Uu]nidentified"

unidentified, Unidentified

"[Uu]ncultured"

uncultured, Uncultured

"[Ii]ncertae[_\\s]?[Ss]edis"

incertae_sedis, Incertae sedis

"^[Mm]etagenome$"

metagenome, Metagenome

"^[Ee]nvironmental"

environmental, Environmental

"^[kpcofgs]__$"

empty QIIME-style rank prefixes

See also

summarize_db(), list_ranks_db()

Author

Adrien Taudière

Examples