Man pages for PAC
Partition-Assisted Clustering and Multiple Alignments of Networks
| aggregateData | Aggregates results from the clustering and merging step. |
| annotateClades | Creates annotation matrix for the clades in aggregated... |
| annotationMatrix_withSubpopProp | Adds subpopulation proportion for the annotation matrix for... |
| BSPLeaveCenter | Finds N Leaf centers in the data |
| constellationPlot | Makes constellation plot, in which the centroids are clusters... |
| fmeasure | F-measure Calculation |
| getAverageSpreadOf2SubpopClades | Calculate the (global) average spread of subpopulations in... |
| getExtraneousCladeSubpopulations | Calculates subpopulations in clades (with two or more... |
| getRepresentativeNetworks | Representative Networks |
| heatmapInput | Creates the matrix that can be easily plotted with a heatmap... |
| JaccardSM | Calculates the Jaccard similarity matrix. |
| MAN | Creates network alignments using network constructed from... |
| MINetwork_matrix_topEdges | Mutual information network connection matrix generation... |
| MINetworkPlot_topEdges | Plots mutual information network (mrnet algorithm) connection... |
| MINetwork_simplified_topEdges | Outputs the vectorized summary of a network based on the... |
| outputNetworks_topEdges_matrix | Wrapper to output the mutual information networks for... |
| outputRepresentativeNetworks_topEdges | Outputs the representative/clade networks (plots and summary... |
| PAC | Partition Assisted Clustering PAC 1) utilizes dsp or bsp-ll... |
| recordWithinClusterSpread | Calculates the within cluster spread |
| refineSubpopulationLabels | Refines the subpopulation labels from PAC using network... |
| renamePrunedSubpopulations | Prune away specified subpopulations in clades that are far... |
| runElbowPointAnalysis | Runs elbow point analysis to find the practical optimal... |
| samplePass | Run PAC for Specified Samples |
