peptideIntensityPlot {qPLEXanalyzer} | R Documentation |
Plots all the peptide intensities for the selected protein
peptideIntensityPlot(MSnSetObj, ProteinID, ProteinName, combinedIntensities=NULL, selectedSequence=NULL, selectedModifications=NULL)
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) |
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.
An intensity plot for selected protein and associated peptides.
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")