Identify the consensus peptide to master protein mapping across multiple runs

Wrapper function to read in infiles, identify the parsimonious proteins to account for the peptides and then (optionally) compare the new and old master protein assignments

get_parsimony_pep2prot(
  infiles,
  seq_col = "Sequence",
  prot_col = "Protein.Accessions",
  master_prot_col = "Master.Protein.Accessions",
  compare_old_new = TRUE
)

Arguments

infiles

list. Outfiles from PD

seq_col

string Column name for peptide sequence

prot_col

string Column name for protein(s)

master_prot_col

string Column name for master protein(s)

compare_old_new

logical Compare the consensus master protein assignments with the original assignments

Value

Returns an data.frame object which maps peptide sequences to consensus master protein ID(s)

Examples

if (FALSE) {
# The input in this example is 2x peptideGroups.txt outputs from Proteome
# Discoverer. Both files must have the columns (cols) specified. This may require
# re-exporting the peptideGroups.txt file from PD as the "Protein.Accessions"
# column is often not there by default.
get_parsimony_pep2prot(
  list("peptideGroups1.txt", "peptideGroups2.txt"),
  seq_col = "Sequence",
  prot_col = "Protein.Accessions",
  master_prot_col = "Master.Protein.Accessions",
  compare_old_new = TRUE
)

}