mergePeptides {qPLEXanalyzer}R Documentation

Merge identical peptides intensities

Description

Merge identical peptides intensities belonging to same protein to single peptide intensity. This function is especially useful for phosphopeptide analysis.

Usage

mergePeptides(MSnSetObj, summarizationFunction, annotation)

Arguments

MSnSetObj

MSnSet; an object of class MSnSet

summarizationFunction

function; method used to aggregate the peptides. Sum, mean or median

annotation

data.frame; a data.frame of protein annotation of four columns: "Accessions", "Gene", "Description" and "GeneSymbol"

Value

An instance of class "MSnSet".

Examples

data(human_anno)
data(exp3_OHT_ESR1)
MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, metadata=exp3_OHT_ESR1$metadata_qPLEX1,
indExpData=c(7:16), Sequences=2, Accessions=6)
MSnset_P <- mergePeptides(MSnSet_data, sum, human_anno)

[Package qPLEXanalyzer version 1.6.0 Index]