Detect taxa whose representative sequence contains a primer

For each taxon, checks whether the representative sequence in the @refseq slot matches any primer in primers (forward or reverse complement) using IUPAC-aware pattern matching. Taxa embedding a primer are likely chimeric or otherwise artefactual.

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_primer_pq(physeq, primers, verbose = TRUE)

Arguments

physeq

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

primers

(named character vector, required) Primer sequences to search for. IUPAC ambiguity codes are supported (e.g. M, R, Y, N). Names are reported in the matched_primers evidence column.

verbose

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

Value

A contam_tbl with one row per flagged taxon, method = "primer", and the evidence columns matched_primers (comma-separated primer names) and n_reads. Empty when no taxon embeds a primer.

See also

filter_contam_pq() to remove flagged taxa, MiscMetabar::cutadapt_remove_primers() for cutadapt-based primer removal of fastq files.

Author

Adrien Taudière

Examples

library(MiscMetabar)
# Requires a phyloseq object with a populated @refseq slot.
primers <- c(
  fwd = "CCCTACGGGGTGCASCAG",
  rev = "GGACTACVSGGGTATCTAAT"
)
identify_contam_primer_pq(data_fungi, primers)
#> ℹ primer: flagged 0 of 1420 taxa embedding a primer.
#> ✔ contam_tbl: no flagged taxa.
#> # A tibble: 0 × 4
#> # ℹ 4 variables: taxon <chr>, method <chr>, matched_primers <chr>,
#> #   n_reads <dbl>