Remove chimeric taxa in one step

A convenience wrapper that runs identify_contam_chimera_pq() and then filter_contam_pq(), returning the chimera-free phyloseq object directly. Chimera removal is a near-ubiquitous cleaning step, so it gets a dedicated verb; the other contaminant methods are composed explicitly via their identify_contam_*_pq() detector and filter_contam_pq().

Usage

filter_chimera_pq(
  physeq,
  method = c("dada2", "vsearch_ref"),
  clean_phyloseq_object = TRUE,
  verbose = TRUE,
  ...
)

Arguments

physeq

(phyloseq, required) A phyloseq object with a populated @refseq slot containing DNA sequences.

method

(character, default "dada2") Detection engine, passed to identify_contam_chimera_pq(): "dada2" (de novo) or "vsearch_ref" (reference-based UCHIME, requires database).

clean_phyloseq_object

(logical, default TRUE) Whether to clean the result with MiscMetabar::clean_pq().

verbose

(logical, default TRUE) Whether to report detection and removal.

...

Additional arguments passed to identify_contam_chimera_pq() (e.g. dada2_method, database, vsearchpath, vsearch_args).

Value

A phyloseq object with chimeric taxa removed (unchanged when none are detected).

See also

identify_contam_chimera_pq() to inspect chimeras before removal, filter_contam_pq() for the general removal verb.

Author

Adrien Taudière

Examples

library(MiscMetabar)
data(data_fungi)
# \donttest{
data_nochim <- filter_chimera_pq(data_fungi, method = "dada2")
#> ℹ chimera (dada2): flagged 450 of 1420 taxa.
#> ! Removing 450 contaminant taxons flagged by methods "chimera".
# }