pickPeptide {ComPrAn} | R Documentation

## 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)

[Package ComPrAn version 1.2.0 Index]