AnnotationParams-class
                        Class '"AnnotationParams"'
GenRegRes-class         Class '"GenRegRes"' and '"ThetaRegRes"'
MLearn,formula,MSnSet,learnerSchema,numeric-method
                        The 'MLearn' interface for machine learning
addLegend               Adds a legend
addLegend_v1            Adds a legend
addMarkers              Adds markers to the data
checkFeatureNamesOverlap
                        Check feature names overlap
checkFvarOverlap        Compare a feature variable overlap
chi2-methods            The PCP 'chi square' method
empPvalues              Estimate empirical p-values for Chi^2 protein
                        correlations.
exprsToRatios-methods   Calculate all ratio pairs
filterBinMSnSet         Filter a binary MSnSet
filterZeroCols          Remove 0 columns/rows
getGOFromFeatures       Retrieve GO terms for feature names
getMarkerClasses        Returns the organelle classes in an 'MSnSet'
getMarkers              Returns the organelle markers in an 'MSnSet'
getPredictions          Returns the predictions in an 'MSnSet'
getStockcol             Manage default colours and point characters
highlightOnPlot         Highlight features of interest on a plot2D
                        figure
knnClassification       knn classification
knnOptimisation         knn parameter optimisation
knntlClassification     knn transfer learning classification
knntlOptimisation       theta parameter optimisation
ksvmClassification      ksvm classification
ksvmOptimisation        ksvm parameter optimisation
lopims                  A complete LOPIMS pipeline
makeGoSet               Creates a GO feature 'MSnSet'
makeNaData              Create a data with missing values
markerMSnSet            Extract marker/unknown subsets
minClassScore           Updates classes based on prediction scores
minMarkers              Creates a reduced marker variable
nbClassification        nb classification
nbOptimisation          nb paramter optimisation
nndist-methods          Nearest neighbour distances
nnetClassification      nnet classification
nnetOptimisation        nnet parameter optimisation
pRolocmarkers           Organelle markers
perTurboClassification
                        perTurbo classification
perTurboOptimisation    PerTurbo parameter optimisation
phenoDisco              Runs the 'phenoDisco' algorithm.
plot2D                  Plot organelle assignment data and results.
plot2D_v1               Plot organelle assignment data and results.
plotDist                Plots the distribution of features across
                        fractions
plsdaClassification     plsda classification
plsdaOptimisation       plsda parameter optimisation
rfClassification        rf classification
rfOptimisation          svm parameter optimisation
sampleMSnSet            Extract a stratified sample of an 'MSnSet'
showGOEvidenceCodes     GO Evidence Codes
svmClassification       svm classification
svmOptimisation         svm parameter optimisation
testMSnSet              Create a stratified 'test' 'MSnSet'
testMarkers             Tests marker class sizes
thetas                  Draw matrix of thetas to test
undocumented            Undocumented/unexported entries
