Compare multiple enzymes on a single protein

compare_digests() runs evaluate_digest() for each enzyme in enzymes and returns a tibble of scores sorted by composite_score descending. Main model-ranking function for pre-acquisition enzyme review.

Usage

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

Arguments

sequence

A single-protein input. Accepts the same forms as digest_protein() but must resolve to exactly one protein. If NULL or empty, raises an error.

enzymes

Character vector of unique enzyme names to compare. Defaults to c("trypsin", "lysc"). Each name must be one of pepVet's supported cleaver-compatible enzyme names.

missed_cleavages

Maximum missed cleavages passed to digest_protein() for every enzyme. Defaults to 1L.

proteome

Optional proteome digest tibble passed to score_peptides() for all enzyme evaluations. When NULL (default), no uniqueness scoring.

weights

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

...

Additional arguments passed to evaluate_digest(). This includes scoring arguments such as gravy_range, length_range, and include_pI, plus include_cleavage_efficiency when peptide-level cleavage annotations are requested during comparison.

Value

A tibble with one row per enzyme and columns enzyme followed by the score columns returned by evaluate_digest(), sorted by composite_score descending.

Limitations

Single-protein only. Use batch_compare_enzymes() for proteome-wide enzyme comparison.

See also

evaluate_digest(), recommend_enzyme()

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

Examples

bsa_path <- system.file("extdata", "P02769.fasta", package = "pepVet")
compare_digests(bsa_path, enzymes = c("trypsin", "lysc"))
#> # A tibble: 2 × 13
#>   enzyme protein_id S_length S_coverage S_count S_hydro S_charge composite_score
#>   <chr>  <chr>         <dbl>      <dbl>   <dbl>   <dbl>    <dbl>           <dbl>
#> 1 tryps… sp|P02769…    0.688      0.997       1   0.769    0.778           0.885
#> 2 lysc   sp|P02769…    0.628      0.857       1   0.763    0.776           0.823
#> # ℹ 5 more variables: verdict <chr>, median_peptide_length <dbl>,
#> #   preset_used <chr>, n_high_efficiency_sites <int>,
#> #   n_low_efficiency_sites <int>