getNormTable: Get normalised table for all proteins

In Scavetta/ComPrAn: Complexome Profiling Analysis package

Get normalised table for all proteins

Description

Extracts values for representative peptides for each protein, for both scenario A and scenario B. Results are combined into one data frame in a format either indended for further analysis or for export.

Usage

getNormTable(.listDf, purpose = "analysis")

Arguments

.listDf	list of data frames
purpose	character, purpose of use of function output, values either "analysis" of "export"

Value

dataframe

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 table with normalised protein values for both scenarios
forAnalysis <- getNormTable(peptide_index,purpose = "analysis")

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