Flag taxa whose genus belongs to a known-contaminant blocklist

Flag taxa whose genus matches a blocklist of known reagent and laboratory contaminants. Unlike contam_corr_pq() (which infers contaminants from the reads-vs-depth relationship) and neg_control_classify_pq() (which uses negative-control occurrence patterns), this method relies solely on taxonomy and therefore needs no negative controls. It is best used as a complementary, curation-oriented filter – review flagged taxa before removal, as several blocklist genera also occur as genuine environmental taxa.

Usage

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) If TRUE, print a cli summary of the flagged taxa.

Value

A named list with four elements:

stats

A data.frame with one row per taxon: taxon, genus, is_known_contaminant, total_reads, prevalence.

contaminants

The subset of stats flagged as contaminants.

blocklist

The genus vector actually used.

summary

A named numeric vector summarizing the result.

See also

known_contaminant_genera(), contam_corr_pq(), neg_control_classify_pq()

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.
res <- contam_blocklist_pq(data_fungi, extra_genera = "Mortierella")
#> ✔ Known-contaminant blocklist summary:
#> • Blocklist genera: 84
#> • Taxa flagged: 1 of 1420 (0.1%)
#> • Reads in flagged taxa: 118
res$summary
#>         taxa_total     n_contaminants   pct_contaminants reads_contaminants 
#>             1420.0                1.0                0.1              118.0 
#>     blocklist_size 
#>               84.0 
head(res$contaminants)
#>     taxon       genus is_known_contaminant total_reads prevalence
#> 1 ASV1215 Mortierella                 TRUE         118          1
# }