Remove contaminant taxa flagged by a detector

The single removal verb for contamination handling. It consumes any contam_tbl produced by an identify_contam_*_pq() detector (or several, combined with rbind()) and prunes the flagged taxa from physeq by name. When the contam_tbl is empty, physeq is returned unchanged.

Usage

filter_contam_pq(physeq, contam, clean_phyloseq_object = TRUE, verbose = TRUE)

Arguments

physeq

(phyloseq, required) A phyloseq object.

contam

(contam_tbl, required) Output of an identify_contam_*_pq() detector. Removal is keyed on the taxon column, so taxa are matched by name rather than position.

clean_phyloseq_object

(logical, default TRUE) Whether to clean the resulting object with MiscMetabar::clean_pq() to drop emptied taxa/samples.

verbose

(logical, default TRUE) Whether to report how many taxa were removed.

Value

A phyloseq object with the flagged taxa removed.

See also

identify_contam_corr_pq() and the other identify_contam_*_pq() detectors that produce a contam_tbl.

Author

Adrien Taudière

Examples

library(MiscMetabar)
# \donttest{
flagged <- identify_contam_corr_pq(data_fungi, verbose = FALSE)
data_clean <- filter_contam_pq(data_fungi, flagged)
#> ✔ No contaminant taxa to remove.
# }