gammaTest: Test gamma clustering parameters

In aarkatkar/gelClust: Clustering and pathway analysis using exponential distributions

Test gamma clustering parameters

Description

Test a range of values for the parameter, n, which represents an upper bound on the number of clusters to find. Optimal clustering is achieved at the parameter that minimizes the modified partition entropy.

Usage

gammaTest(start, end, gm, maxiter = 200)

Arguments

start	the lower bound of the tested range.
end	the upper bound of the tested range.
gm	the output of a gelMatrix call.
maxiter	the maximum iterations of the clustering algorithm for each test.

Value

A plot where a blue star indicates the minimum. A red "x" denotes a test where convergence was not reached before the maximum iterations.

Author(s)

Anooj Arkatkar

See Also

gammaCluster

Examples

  data(foldChange)
  gm <- gelMatrix(foldChange)
  gammaTest(2, 15, gm)

aarkatkar/gelClust documentation built on May 6, 2022, 12:24 a.m.