rv.pval: Determining a p-value the (partial) RV coefficient

In iTOP: Inferring the Topology of Omics Data

Description

This function uses a permutation test to determine a p-value for the RV coefficient RV(a, b) or the partial RV coefficient RV(a, b | set).

Usage

rv.pval(cors, cors_perm, a, b, set = NULL)

Arguments

cors	The result from rv.cor.matrix().
cors_perm	The result from run.permutations().
a	Either an index or a string to identify dataset a.
b	Either an index or a string to identify dataset b.
set	Optional parameter to define the datasets that need to be partialized for. If set consists of one dataset, then provide an index or a string to identify set. If set consists of multiple datasets, then provide a vector of indices or a vector of strings.

Value

The p-value.

Examples

set.seed(2)
n = 100
p = 100
x1 = matrix(rnorm(n*p), n, p)
x2 = x1 + matrix(rnorm(n*p), n, p)
x3 = x2 + matrix(rnorm(n*p), n, p)
data = list(x1=x1, x2=x2, x3=x3)
config_matrices = compute.config.matrices(data)
cors = rv.cor.matrix(config_matrices)
cors_perm = run.permutations(config_matrices, nperm=1000)
rv.pval(cors, cors_perm, "x1", "x3", "x2")

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