addLegend               Adds a legend
addMarkers              Adds markers to the data
AnnotationParams-class
                        Class '"AnnotationParams"'
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
ClustDist-class         Class '"ClustDist"'
ClustDistList-class     Storing multiple ClustDist instances
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
GenRegRes-class         Class '"GenRegRes"' and '"ThetaRegRes"'
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'
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
MAPParams-class         The 'logPosteriors' function can be used to
                        extract the log-posteriors at each iteration of
                        the EM algorithm to check for convergence.
markerMSnSet            Extract marker/unknown subsets
MartInstance-class      Class '"MartInstance"'
mcmc_get_outliers       Number of outlier at each iteration of MCMC
MCMCChains-class        Instrastructure to store and process MCMC
                        results
minMarkers              Creates a reduced marker variable
mixing_posterior_check
                        Model calibration plots
MLearn,formula,MSnSet,learnerSchema,numeric-method
                        The 'MLearn' interface for machine learning
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
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
pRolocmarkers           Organelle markers
QSep-class              Quantify resolution of a spatial proteomics
                        experiment
rfClassification        rf classification
rfOptimisation          svm parameter optimisation
sampleMSnSet            Extract a stratified sample of an 'MSnSet'
setLisacol              Manage default colours and point characters
spatial2D               Uncertainty plot in localisation probabilities
SpatProtVis-class       Class 'SpatProtVis'
subsetMarkers           Subsets markers
svmClassification       svm classification
svmOptimisation         svm parameter optimisation
tagmMcmcTrain           Localisation of proteins using the TAGM MCMC
                        method
testMarkers             Tests marker class sizes
testMSnSet              Create a stratified 'test' 'MSnSet'
thetas                  Draw matrix of thetas to test
undocumented            Undocumented/unexported entries
zerosInBinMSnSet        Compute the number of non-zero values in each
                        marker classes
