peptideIntensityPlot {qPLEXanalyzer} | R Documentation

## Plot peptide intensities

### Description

Plots all the peptide intensities for the selected protein

### Usage

    peptideIntensityPlot(MSnSetObj, ProteinID, ProteinName,
                                     combinedIntensities=NULL, selectedSequence=NULL,
                                     selectedModifications=NULL)

### Arguments

`MSnSetObj` | MSnSet; an object of class MSnSet containing peptide level intensities
`ProteinID` | character: Uniprot ID of the protein
`ProteinName` | character: name of the protein
`combinedIntensities` | MSnSet; an object of class MSnSet containing protein level intensities
`selectedSequence` | character: sequence present in the "Sequences" column in fData(MSnSetObj)
`selectedModifications` | character: modification present in the "Modifications" column in fData(MSnSetObj)

### Details

Providing a summarised protein level MSnSet object to the 'combinedIntensities' argument will add a summed protein intensity trace to the plot along with the peptide intensities.

### Value

An intensity plot for selected protein and associated peptides.

### 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 <- summarizeIntensities(MSnSet_data, sum, human_anno)
    peptideIntensityPlot(MSnSet_data, combinedIntensities=MSnset_P, ProteinID="P03372", ProteinName= "ESR1")

[Package qPLEXanalyzer version 1.5.0 Index]