Calculate genetic distance from genealogy or VAF — dist_genealogy • tumopp

Calculate genetic distance from genealogy or VAF

Usage

dist_genealogy(graph, cell_ids)

dist_vaf(vaf, ncell = Inf)

pairwise_distances(graph, regions)

Arguments

graph: igraph
cell_ids: id column of sampled regions
vaf: data.frame or matrix. e.g., output from make_vaf().
ncell: number of cells per specimen
regions: output of sample_uniform_regions()

Details

dist_genealogy summarizes branch lengths within/between regions.

dist_vaf summarizes diversity within/between regions.

pairwise_distances summarizes physical and genetic distances.

See also