mergePeptides: Merge identical modified peptides intensities

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

Merge identical modified peptides intensities

Description

Merge modified peptides with identical sequences to single peptide intensity. This function is especially useful for modified peptide enrichment based method such as phosphopeptide analysis.

Usage

mergePeptides(MSnSetObj, summarizationFunction, annotation, keepCols = NULL)

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"
keepCols	a vector of additional columns from fData(MSnSetObj) to keep. either be a numeric vector of column indices or a character vector of column names

Details

Rows of the intensity matrix with identical peptide sequences are merged by summarising the intensities using summarizationFunction.

Columns specified with keepCols are retained in the final output. Non-unique entries in different rows are concatenated with ';'.

Value

An object of class MSnSet (see MSnSet-class)

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)

crukci-bioinformatics/qPLEXanalyzer documentation built on Sept. 24, 2024, 1:13 a.m.