BSPLeaveCenter          Finds N Leaf centers in the data
JaccardSM               Calculates the Jaccard similarity matrix.
MAN                     Creates network alignments using network
                        constructed from subpopulations after PAC
MINetworkPlot_topEdges
                        Plots mutual information network (mrnet
                        algorithm) connection using the parmigene
                        package. Mutual information calculated with
                        infotheo package.
MINetwork_matrix_topEdges
                        Mutual information network connection matrix
                        generation (mrnet algorithm) using the
                        parmigene package. Mutual information
                        calculated with infotheo package.
MINetwork_simplified_topEdges
                        Outputs the vectorized summary of a network
                        based on the number of edges connected to a
                        node
PAC                     PAC (Partition Assisted Clustering)
aggregateData           Aggregates results from the clustering and
                        merging step.
annotateClades          Creates annotation matrix for the clades in
                        aggregated format. The matrix contains average
                        signals of each dimension for each clade in
                        each sample
annotationMatrix_withSubpopProp
                        Adds subpopulation proportion for the
                        annotation matrix for the clades
fmeasure                Compute the F measure between the ground truth
                        and the estimated label
getRepresentativeNetworks
                        Outputs representative networks for
                        clades/subpopulations larger than a size filter
                        (very small subpopulations are not considered
                        in downstream analyses)
heatmapInput            Creates the matrix that can be easily plotted
                        with a heatmap function available in an R
                        package
outputNetworks_topEdges_matrix
                        Wrapper to output the mutual information
                        networks for subpopulations with size larger
                        than a desired threshold.
outputRepresentativeNetworks_topEdges
                        Outputs the representative/clade networks
                        (plots and summary vectors) for subpopulations
                        with size larger than a desired threshold.
                        Saves the networks and the data matrices
                        without the smaller subpopulations.
refineSubpopulationLabels
                        Refines the subpopulation labels from PAC using
                        network alignment and small subpopulation
                        information. Outputs a new set of files
                        containing the representative labels.
samplePass              A wrapper to run PAC and output subpopulation
                        mutual information networks.
