peptideIntensityPlot: Plot peptide intensities

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

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")

crukci-bioinformatics/qPLEXanalyzer documentation built on Oct. 23, 2023, 2:27 a.m.