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Functions for protein group inference, inspired by the concepts from "MaxQuant's post-computational razor: a massively parallel graphical model for post-processing proteomics data" by K. S. Rudolph et al.

Source: R/protgroup_assembly.R
default_protein_grouping.Rd

The main function is assemble_protein_groups, which takes a peptide-to-protein mapping and assembles protein groups based on shared peptides. Default rule for merging proteins into a single group

Usage

default_protein_grouping(
  pepgroup_to_pepgroup,
  nspec_peptides = 1L,
  rspec_peptides = NA_real_
)

Arguments

pepgroup_to_pepgroup

a data frame of peptide-sharing protein group candidates

nspec_peptides

Number of specific peptides threshold.

rspec_peptides

Fraction of specific peptides threshold.

Value

filtered pepgroup_to_pepgroup frame with pairs of protein group candidates to merge

See also

assemble_protein_groups()

pregrouped_protein_grouping()