Detect taxa whose genus belongs to a known-contaminant blocklist

Flags taxa whose genus matches a blocklist of known reagent and laboratory contaminants. A taxonomy-only method requiring no negative controls, best used as a complementary, curation-oriented filter – review flagged taxa before removal, as several blocklist genera also occur as genuine environmental taxa.

This is a pure detector: it flags taxa and returns a contam_tbl without modifying physeq. Use filter_contam_pq() to remove the flagged taxa.

Usage

identify_contam_blocklist_pq(
  physeq,
  genus_blocklist = known_contaminant_genera(),
  tax_rank = "Genus",
  extra_genera = NULL,
  ignore_case = TRUE,
  verbose = TRUE
)

Arguments

physeq

(phyloseq, required) A phyloseq object with a tax_table.

genus_blocklist

(character, default known_contaminant_genera()) Vector of genus names to flag.

tax_rank

(character, default "Genus") Name of the tax_table column holding genus-level assignments.

extra_genera

(character, default NULL) Additional genus names to append to genus_blocklist.

ignore_case

(logical, default TRUE) If TRUE, matching is case-insensitive.

verbose

(logical, default TRUE) Print a one-line detection summary.

Value

A contam_tbl with one row per flagged taxon, method = "blocklist", and the evidence columns genus, total_reads, and prevalence. Empty when no genus matches the blocklist.

See also

known_contaminant_genera() for the default blocklist, filter_contam_pq() to remove flagged taxa.

Author

Adrien Taudière

Examples

library(MiscMetabar)
data(data_fungi)
# \donttest{
# data_fungi is fungal, so the default bacterial blocklist matches nothing;
# extend it with a genus present in the data for illustration.
identify_contam_blocklist_pq(data_fungi, extra_genera = "Mortierella")
#> ℹ blocklist: flagged 1 of 1420 taxa from 84 blocklist genera.
#> contam_tbl: 1 flagged taxon from method "blocklist"
#> # A tibble: 1 × 5
#>   taxon   method    genus       total_reads prevalence
#>   <chr>   <chr>     <chr>             <dbl>      <dbl>
#> 1 ASV1215 blocklist Mortierella         118          1
# }