Return the highest-scoring enzyme for a single protein

recommend_enzyme() calls compare_digests() and returns the name of the enzyme with the highest composite score. When two or more enzymes are tied, all tied enzyme names are returned in alphabetical order. It is a compact model-ranking result for scripted triage that stays aligned with compare_digests().

Usage

recommend_enzyme(
  sequence,
  enzymes = c("trypsin", "lysc"),
  missed_cleavages = 1L,
  proteome = NULL,
  weights = NULL,
  ...
)

Arguments

sequence

A single-protein input passed to compare_digests(). If NULL or empty, raises an error.

enzymes

Character vector of unique enzyme names to compare. Defaults to c("trypsin", "lysc").

missed_cleavages

Maximum missed cleavages. Defaults to 1L.

proteome

Optional proteome digest tibble for uniqueness scoring. When NULL (default), no uniqueness scoring.

weights

Optional scoring weight vector. When NULL (default), uses pepVet's default scoring weights.

...

Additional scoring arguments passed to compare_digests() and ultimately to evaluate_digest() and score_peptides().

Value

A character vector of one or more enzyme names. Length greater than one only when top scores are tied within floating-point tolerance.

Limitations

Single-protein only. When multiple enzymes tie within tolerance, all are returned in alphabetical order with no further tie-breaking. The result is not an experimental recommendation.

See also

compare_digests(), evaluate_digest()

Other evaluation: batch_compare_enzymes(), batch_evaluate(), compare_digests(), evaluate_digest(), sensitivity_analysis(), summarize_batch(), triage_proteins()

Examples

bsa_path <- system.file("extdata", "P02769.fasta", package = "pepVet")
recommend_enzyme(bsa_path, enzymes = c("trypsin", "lysc"))
#> [1] "trypsin"