EB_module: EB_module function

In azolling/EBmodules:

Description

This function is the main function of the package. It computes the common gene modules for a collection of correlation matrices

Usage

EB_module(R, gap = FALSE, k = 500, scattered = FALSE,
  method_scattered = c("GPD", "kmeans"), Kmin = NULL, Kmax = NULL,
  Nperm = 100, dicho_f = 2)

Arguments

R	is a list of lenght L1 (number of studies) of correlation matrices of the same size
gap	whether to use the gap statistic to determine the optimal number of clusters
k	if gap is TRUE then k=NULL otherwise, k is an integer indicating the number of desired modules (scattered genes do not count as a module)
scattered:	bolean whether the function should look for scattered genes before looking for modules.

Value

common_r the common correlation matrix estimated through the empirical bayesian model

modules a list of modules with the scattered genes grouped inside a module (called -1)

bestk the optimal number of modules according to a modified version of the GAP statistic (if gap is set to TRUE)

azolling/EBmodules documentation built on May 11, 2019, 5:17 p.m.