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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

# From a FASTA file (no unwanted values in example data)
db <- system.file("extdata", "example_unite.fasta", package = "dbpq")
count_unwanted_tax(db)
#> No unwanted taxonomic values found.
#> # A tibble: 0 × 5
#> # ℹ 5 variables: pattern <chr>, description <chr>, rank <chr>, n_matches <int>,
#> #   example_values <chr>

if(requireNamespace("MiscMetabar", quietly = TRUE)) {
 ref_fasta <- Biostrings::readDNAStringSet(system.file("extdata",
   "mini_UNITE_fungi.fasta.gz",
   package = "MiscMetabar", mustWork = TRUE
 ))
data("data_fungi_mini", package = "MiscMetabar")
physeq_new <- MiscMetabar::assign_mmseqs2(
   MiscMetabar::data_fungi_mini,
   ref_fasta = ref_fasta,
   behavior = "add_to_phyloseq"
 )
count_unwanted_tax(physeq_new)
}
#> Found 42 unwanted value(s) matching 1 pattern(s) across 4 rank(s).
#> Tip: use MiscMetabar::verify_tax_table() to clean these values in your phyloseq object.
#> # A tibble: 4 × 5
#>   pattern                      description    rank      n_matches example_values
#>   <chr>                        <chr>          <chr>         <int> <chr>         
#> 1 "[Ii]ncertae[_\\s]?[Ss]edis" incertae sedis Family            4 Cantharellale…
#> 2 "[Ii]ncertae[_\\s]?[Ss]edis" incertae sedis Order_mm…         2 Agaricomycete…
#> 3 "[Ii]ncertae[_\\s]?[Ss]edis" incertae sedis Family_m…        15 Trechisporale…
#> 4 "[Ii]ncertae[_\\s]?[Ss]edis" incertae sedis Genus_mm…        21 Tricholomatac…