Find taxa whose reference sequences match primer sequences

Searches every sequence in @refseq for occurrences of the supplied primers (forward and reverse complement) using IUPAC-aware matching via Biostrings::vcountPattern(). Returns a data frame of taxa that match at least one primer, which can be passed directly to tidypq::filter_taxa_pq() to prune them from the phyloseq object.

Usage

find_primers_pq(physeq, primers, verbose = TRUE)

Arguments

physeq

(required) A phyloseq::phyloseq object with a populated @refseq slot.

primers

(required) A named character vector of primer sequences. IUPAC ambiguity codes (M, R, Y, S, W, K, B, D, H, V, N) are supported.

verbose

(logical, default TRUE) If TRUE, print a summary message.

Value

A data.frame (or NULL if no matches) with columns:

taxon

Character. Taxa name as in taxa_names(physeq).

matched_primers

Character. Comma-separated names of matching primers.

n_reads

Numeric. Total read count across all samples (phyloseq::taxa_sums(physeq)).

Details

Author

Adrien Taudière

Examples

primers <- c(
  mcrA_fwd = "GGTGGTGTMGGDTTCACMCARTA",
  mcrA_rev = "CGTTCATBGCGTAGTTVGGRTAGT"
)
bad <- find_primers_pq(data_fungi_mini, primers)
#> 0 taxa matched at least one primer out of 45.
bad
#> NULL

# Prune contaminated taxa (requires tidypq):
# if (!is.null(bad)) {
#   tidypq::filter_taxa_pq(
#     data_fungi_mini,
#     !taxa_names(data_fungi_mini) %in% bad$taxon,
#     clean_phyloseq_object = TRUE
#   )
# }