MAN {PAC}

Creates network alignments using network constructed from subpopulations after PAC

Description

Creates network alignments using network constructed from subpopulations after PAC

Usage

MAN(sampleIDs, num_PACSupop, smallSubpopCutoff, k_clades)

Arguments

sampleIDs

sampleID vector

num_PACSupop

number of subpopulations learned in PAC step for each sample

smallSubpopCutoff

Population size cutoff for subpopulations in clade calculation. The small subpopulations will be considered in the refinement step.

k_clades

number of clades to output before refinement

Value

clades_network_only the clades constructed without small subpopulations (by cutoff) using mutual information network alignments