Partition-Assisted Clustering and Multiple Alignments of Networks

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Documentation for package ‘PAC’ version 1.1.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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
BSPLeaveCenter	Finds N Leaf centers in the data
constellationPlot	Makes constellation plot, in which the centroids are clusters are embedded in the t-SNE 2D plane and the cross-sample relationships are plotted as lines connecting related sample clusters (clades).
fmeasure	F-measure Calculation
getAverageSpreadOf2SubpopClades	Calculate the (global) average spread of subpopulations in clades with 2 subpopulations on the constellation plot.
getExtraneousCladeSubpopulations	Calculates subpopulations in clades (with two or more subpopulations) that are too far away from other subpopulations (within the same clade) on the constellation plot; these far away subpopulations should be pruned away from the original clades.
getRepresentativeNetworks	Representative Networks
heatmapInput	Creates the matrix that can be easily plotted with a heatmap function available in an R package
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
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.
PAC	Partition Assisted Clustering PAC 1) utilizes dsp or bsp-ll to recursively partition the data space and 2) applies a short round of kmeans style postprocessing to efficiently output clustered labels of data points.
recordWithinClusterSpread	Calculates the within cluster spread
refineSubpopulationLabels	Refines the subpopulation labels from PAC using network alignment and small subpopulation information. Outputs a new set of files containing the representative labels.
renamePrunedSubpopulations	Prune away specified subpopulations in clades that are far away.
runElbowPointAnalysis	Runs elbow point analysis to find the practical optimal number of clades to output. Outputs the average within sample cluster spread for all samples and the elbow point analysis plot with loess line fitted through the results.
samplePass	Run PAC for Specified Samples