Triage proteins from a batch evaluation

triage_proteins() appends an action column to the flat tibble returned by batch_evaluate() with deterministic action labels based on each protein's verdict and difficulty flags.

Usage

triage_proteins(batch_result)

Arguments

batch_result

A tibble returned by batch_evaluate(). If NULL or empty, raises an error.

Value

A tibble with one row per protein containing all score and flag columns from the flat batch summary, plus an action column. Possible values:

"proceed"

Good verdict. No intervention indicated.

"consider_alternative"

Moderate verdict without a sequence-level difficulty flag. Review component scores and consider a preset or missed-cleavage adjustment.

"try_other_enzyme"

Moderate or Poor verdict with flag_hydrophobic or flag_short_protein, or any Poor verdict without an intrinsic complexity flag. This action marks the protein for an explicit alternative-enzyme comparison.

"skip"

No valid peptides or a low-complexity sequence. This action marks the row for manual review rather than asserting that another enzyme cannot help.

Limitations

Triage actions are advisory, based on heuristic difficulty flags from the batch score columns. They do not re-evaluate the protein with alternative enzymes. Use compare_digests() for that.

See also

batch_evaluate(), summarize_batch()

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

Examples

small_path <- system.file(
  "extdata", "small_proteome_50_proteins.fasta",
  package = "pepVet"
)
batch <- batch_evaluate(small_path, enzyme = "trypsin")
triaged <- triage_proteins(batch)
table(triaged$action)
#> 
#> consider_alternative              proceed                 skip 
#>                    9                   40                    1