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 object created by `ggplot`

### 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 1.8.2 Index]