AnnotationParams-class
                        Class '"AnnotationParams"'
ClustDist-class         Class '"ClustDist"'
ClustDistList-class     Storing multiple ClustDist instances
GenRegRes-class         Class '"GenRegRes"' and '"ThetaRegRes"'
MAPParams-class         The 'logPosteriors' function can be used to
                        extract the log-posteriors at each iteration of
                        the EM algorithm to check for convergence.
MCMCChains-class        Instrastructure to store and process MCMC
                        results
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.
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
makeGoSet               Creates a GO feature 'MSnSet'
markerMSnSet            Extract marker/unknown subsets
mcmc_get_outliers       Number of outlier at each iteration of MCMC
minMarkers              Creates a reduced marker variable
mixing_posterior_check
                        Model calibration plots
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
nicheMeans2D            Uncertainty plot organelle means
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
plotConsProfiles        Plot marker consensus profiles.
plotDist                Plots the distribution of features across
                        fractions
plotEllipse             A function to plot probabiltiy ellipses on
                        marker PCA plots to visualise and assess TAGM
                        models.
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
spatial2D               Uncertainty plot in localisation probabilities
subsetMarkers           Subsets markers
svmClassification       svm classification
svmOptimisation         svm parameter optimisation
tagmMcmcTrain           Localisation of proteins using the TAGM MCMC
                        method
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
