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 |
selectedModifications |
character: modification present in the
"Modifications" column in |
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 object created by ggplot
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")