Man pages for PAC
Partition-Assisted Clustering and Multiple Alignments of Networks

aggregateDataAggregates results from the clustering and merging step.
annotateCladesCreates annotation matrix for the clades in aggregated...
annotationMatrix_withSubpopPropAdds subpopulation proportion for the annotation matrix for...
BSPLeaveCenterFinds N Leaf centers in the data
constellationPlotMakes constellation plot, in which the centroids are clusters...
fmeasureF-measure Calculation
getAverageSpreadOf2SubpopCladesCalculate the (global) average spread of subpopulations in...
getExtraneousCladeSubpopulationsCalculates subpopulations in clades (with two or more...
getRepresentativeNetworksRepresentative Networks
heatmapInputCreates the matrix that can be easily plotted with a heatmap...
JaccardSMCalculates the Jaccard similarity matrix.
MANCreates network alignments using network constructed from...
MINetwork_matrix_topEdgesMutual information network connection matrix generation...
MINetworkPlot_topEdgesPlots mutual information network (mrnet algorithm) connection...
MINetwork_simplified_topEdgesOutputs the vectorized summary of a network based on the...
outputNetworks_topEdges_matrixWrapper to output the mutual information networks for...
outputRepresentativeNetworks_topEdgesOutputs the representative/clade networks (plots and summary...
PACPartition Assisted Clustering PAC 1) utilizes dsp or bsp-ll...
recordWithinClusterSpreadCalculates the within cluster spread
refineSubpopulationLabelsRefines the subpopulation labels from PAC using network...
renamePrunedSubpopulationsPrune away specified subpopulations in clades that are far...
runElbowPointAnalysisRuns elbow point analysis to find the practical optimal...
samplePassRun PAC for Specified Samples
PAC documentation built on Aug. 16, 2017, 9:04 a.m.