Rule for merging proteins that allows for pre-grouping

Rule for merging proteins that allows for pre-grouping

Usage

pregrouped_protein_grouping(
  pepgroup_to_pepgroup,
  protein_to_pregroup,
  rspec_peptides = NA_real_,
  nspec_peptides = 1,
  pregroup_rspec_peptides = 0.25,
  pregroup_nspec_peptides = 5
)

Arguments

pepgroup_to_pepgroup

a data frame of peptide-sharing protein group candidates

protein_to_pregroup

A named vector mapping protein accessions to pre-group IDs.

rspec_peptides

Fraction of specific peptides threshold.

nspec_peptides

Number of specific peptides threshold.

pregroup_rspec_peptides

Fraction of specific peptides threshold for pre-grouped proteins.

pregroup_nspec_peptides

Number of specific peptides threshold for pre-grouped proteins.

Value

filtered pepgroup_to_pepgroup frame with pairs of protein group candidates to merge

See also

assemble_protein_groups()

default_protein_grouping()