scanKModularity: Scan joint graph modularity for a range of k (or k.self)...

In conos: Clustering on Network of Samples

Scan joint graph modularity for a range of k (or k.self) values Builds graph with different values of k (or k.self if scan.k.self=TRUE), evaluating modularity of the resulting multilevel clustering NOTE: will run evaluations in parallel using con$n.cores (temporarily setting con$n.cores to 1 in the process)

Description

Scan joint graph modularity for a range of k (or k.self) values Builds graph with different values of k (or k.self if scan.k.self=TRUE), evaluating modularity of the resulting multilevel clustering NOTE: will run evaluations in parallel using con$n.cores (temporarily setting con$n.cores to 1 in the process)

Usage

scanKModularity(
  con,
  min = 3,
  max = 50,
  by = 1,
  scan.k.self = FALSE,
  omit.internal.edges = TRUE,
  verbose = TRUE,
  plot = TRUE,
  ...
)

Arguments

con	Conos object to test
min	numeric Minimal value of k to test (default=3)
max	numeric Value of k to test (default=50)
by	numeric Scan step (default=1)
scan.k.self	boolean Whether to test dependency on scan.k.self (default=FALSE)
omit.internal.edges	boolean Whether to omit internal edges of the graph (default=TRUE)
verbose	boolean Whether to provide verbose output (default=TRUE)
plot	boolean Whether to plot the output (default=TRUE)
...	other parameters will be passed to con$buildGraph()

Value

a data frame with $k $m columns giving k and the corresponding modularity

conos documentation built on May 29, 2024, 9:56 a.m.