get_parsimony_pep2prot: Identify the consensus peptide to master protein mapping...

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

Identify the consensus peptide to master protein mapping across multiple runs

Description

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

Usage

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

## Not run: 
# 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
)


## End(Not run)

CambridgeCentreForProteomics/camprotR documentation built on Jan. 27, 2023, 8:36 p.m.