pepvet_preset() returns a named list containing a GRAVY range, peptide
length range, and scoring weights for a supported proteomics workflow.
Presets are intended as editable starting points rather than hard rules.
Their exact ranges and weights are conservative package choices, not
empirically calibrated boundaries.
Value
A named list with gravy_range, length_range, weights, and
include_pI.
The returned object can be passed directly into score_peptides() or
evaluate_digest() through do.call() or argument splicing.
Presets
"standard" : Default scoring configuration for routine DDA examples.
Uses the [7, 25] length range, [-1.0, 0.6] GRAVY range, and default
protein-only weights.
"dia" : A wider starting configuration for DIA or SWATH examples.
Uses the [7, 30] length range, [-1.0, 0.8] GRAVY range, and a larger
coverage weight than the standard preset.
"targeted" : A narrower starting configuration for SRM, PRM, or MRM
examples. Uses the [8, 20] length range and [-0.8, 0.4] GRAVY range.
When a background proteome digest is supplied, uniqueness receives 30 percent
of the composite weight.
"membrane" : A wider hydrophobicity configuration for membrane-protein
review. Uses the [7, 30] length range, extends the upper GRAVY boundary to
2.0, and assigns 5 percent of the composite weight to S_hydro.
"ffpe_degraded" : A broader length configuration for exploratory work
with degraded or FFPE-derived material. Uses the [6, 30] length range and
assigns more weight to S_count than the standard preset.
"fractionated" : SCX / high-pH RP fractionation planning. Same
scoring parameters as "standard" but with include_pI = TRUE
to append peptide-level pI values for fractionation-aware analysis.
Limitations
The six presets encode package priors. Inspect the returned values and use explicit arguments when the experimental context calls for other choices.
See also
Other utils:
calculate_pI(),
calculate_peptide_mass()