pickPeptide: Select Top Peptide For Various Scenarios

In Scavetta/ComPrAn: Complexome Profiling Analysis package

Select Top Peptide For Various Scenarios

Description

This function selects a single unique peptide to represent each 'Protein Group Accession' There are 2 ways of selecting peptides, both are perform as they are needed for different tasks later on.

1. Scenario A: select peptide occuring in most fractions, do this individually for labelled/unlabelled (max value for any peptide is equal to number of fractions) in case of ties, pick peptide whith highest 'Precursor Area' in any fraction.

2. Scenario B: select peptide occuring in most fractions counting both label states together (max value for any peptide is equal to twice the number of fractions) in case of ties, pick peptide with highest 'Precursor Area' in any fraction. Representative peptide in Scenario B is picked only for proteins that have shared peptide between label states.

Usage

pickPeptide(.data)

Arguments

.data

a dataframe

Value

list of data frames

Examples

##Use example peptide data set, read in and clean data
inputFile <- system.file("extData", "data.txt", package = "ComPrAn")
peptides <- peptideImport(inputFile)
peptides <- cleanData(peptides, fCol = "Search ID")
## separate chemical modifications and labelling into separate columns
peptides <- splitModLab(peptides) 
## remove unneccessary columns, simplify rows
peptides <- simplifyProteins(peptides) 
## Pick representative peptide for each protein for both scenarios
peptide_index <- pickPeptide(peptides)

Scavetta/ComPrAn documentation built on Oct. 3, 2022, 1:08 a.m.