AnnotationParams-class
                        Class '"AnnotationParams"'
ClustDist-class         Class '"ClustDist"'
ClustDistList-class     Storing multiple ClustDist instances
GenRegRes-class         Class '"GenRegRes"' and '"ThetaRegRes"'
MLearn,formula,MSnSet,learnerSchema,numeric-method
                        The 'MLearn' interface for machine learning
MartInstance-class      Class '"MartInstance"'
QSep-class              Quantify resolution of a spatial proteomics
                        experiment
SpatProtVis-class       Class 'SpatProtVis'
addGoAnnotations        Add GO annotations
addLegend               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
classWeights            Calculate class weights
clustDist               Pairwise Distance Computation for Protein
                        Information Sets
empPvalues              Estimate empirical p-values for Chi^2 protein
                        correlations.
exprsToRatios-methods   Calculate all ratio pairs
fDataToUnknown          Update a feature variable
filterBinMSnSet         Filter a binary MSnSet
filterMaxMarkers        Removes class/annotation information from a
                        matrix of candidate markers that appear in the
                        'fData'.
filterMinMarkers        Removes class/annotation information from a
                        matrix of candidate markers that appear in the
                        'fData'.
filterZeroCols          Remove 0 columns/rows
getGOFromFeatures       Retrieve GO terms for feature names
getMarkerClasses        Returns the organelle classes in an 'MSnSet'
getMarkers              Get the organelle markers in an 'MSnSet'
getNormDist             Extract Distances from a '"ClustDistList"'
                        object
getPredictions          Returns the predictions in an 'MSnSet'
goIdToTerm              Convert GO ids to/from terms
highlightOnPlot         Highlight features of interest on a spatial
                        proteomics plot
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'
markerMSnSet            Extract marker/unknown subsets
minMarkers              Creates a reduced marker variable
move2Ds                 Displays a spatial proteomics animation
mrkConsProfiles         Marker consensus profiles
mrkHClust               Draw a dendrogram of subcellular clusters
mrkVecToMat             Create a marker vector or matrix.
nbClassification        nb classification
nbOptimisation          nb paramter optimisation
nndist-methods          Nearest neighbour distances
nnetClassification      nnet classification
nnetOptimisation        nnet parameter optimisation
orderGoAnnotations      Orders annotation information
orgQuants               Returns organelle-specific quantile scores
pRolocmarkers           Organelle markers
perTurboClassification
                        perTurbo classification
perTurboOptimisation    PerTurbo parameter optimisation
phenoDisco              Runs the 'phenoDisco' algorithm.
plot2D                  Plot organelle assignment data and results.
plot2Ds                 Draw 2 data sets on one PCA plot
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'
setLisacol              Manage default colours and point characters
showGOEvidenceCodes     GO Evidence Codes
subsetMarkers           Subsets markers
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
zerosInBinMSnSet        Compute the number of non-zero values in each
                        marker classes
