compute.config.matrix: Computes a configuration matrix

In iTOP: Inferring the Topology of Omics Data

Description

Given a data matrix, this function computes the configuration matrix for the corresponding dataset. You'll typically won't need to call this function directly, but should use compute.config.matrices() instead, as it will make determining partial RV coefficients, p-values and confidence intervals easier later on.

Usage

compute.config.matrix(x, similarity_fun = inner.product, center = TRUE,
  mod.rv = TRUE)

Arguments

x	Data matrix.
similarity_fun	A function pointer to the similarity function to be used (default=inner.product).
center	A boolean indicating whether centering should be used (default=TRUE).
mod.rv	A boolean indicating whether the modified RV coefficient should be used (default=TRUE).

Value

A configuration matrix.

Examples

set.seed(2)
n = 100
p = 100
x1 = matrix(rnorm(n*p), n, p)
x2 = x1 + matrix(rnorm(n*p), n, p)
S1 = compute.config.matrix(x1)
S2 = compute.config.matrix(x1)
rv.coef(S1, S2)

Example output

     [,1]
[1,]    1

iTOP documentation built on May 2, 2019, 3:44 a.m.