ChemoProtSet-class      An S4 class to run the doscheda pipeline
boxplot,ChemoProtSet-method
                        Default boxplot for objects of class
                        ChemoProtSet
corrPlot                Plot showing correlation between all channels
                        across replicates
densityPlot             Density plot for objects of class ChemoProtSet
doscheda                Doscheda: A package for Down Stream
                        Chemo-Proteomics Data Analysis
doschedaApp             Run shiny application for DOSCHEDA
doschedaData            Peptide Intensity data set for Doscheda
fitModel                Method to fit a model to an object of class
                        'ChemoProtSet'
getDatasets             Accessor function for the datasets slot.
getFinal                Accessor function for the finalData slot.
getInput                Accessor function for the Input
getNorm                 Accessor function for the normData
getParameters           Accessor function for the parameters slot.
makeReport              Create report from 'ChemProtSet' object
meanSdPlot              MeanSd plot for objects of class ChemoProtSet
pcaPlot                 PCA of the main data sets contained in a object
                        of class ChemoProtSet
plot.ChemoProtSet       Default plot for objects of class ChemoProtSet
processedExample        Processed Peptide Intensity data set for
                        Doscheda
removePeptides          Method to remove peptides from input data of an
                        object of class 'ChemoProtSet'
replicatePlot           Plot replicates between concentrations
runDoscheda             Wrapper Function to run the entire Doscheda
                        pipeline
runNormalisation        Method to remove peptides from input data of an
                        object of class 'ChemoProtSet'
setData                 Method for attaching and standardising data for
                        objects of class 'ChemoProtSet'
setParameters           Method to set parameters for a ChemoProtSet
volcanoPlot             Volcano plot for objects of class ChemoProtSet
