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. |