Partition-Assisted Clustering and Multiple Alignments of Networks

Documentation for package ‘PAC’ version 1.0.7

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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
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
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	PAC (Partition Assisted Clustering)
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.