onlyInOneLabelState: Report Proteins Present In Only One Label State

In Scavetta/complexomics: Complexome Profiling Analysis package

Report Proteins Present In Only One Label State

Description

This function returns NAMES of proteins present in only labelled/only unlabelld or both label states

Usage

onlyInOneLabelState(.data)

Arguments

.data

An environment containing dataframes

Value

a list with 3 items, each item is a vector containing names belonging to one of 3 groups

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)
## extract list of names of proteins present in one/both samples
oneStateList <- onlyInOneLabelState(peptide_index)

Scavetta/complexomics documentation built on Oct. 1, 2022, 2:15 a.m.