PermutationTest: Permutation Test for Dissimilarity Matrices

In MantelCorr: Compute Mantel Cluster Correlations

Description

'PermutationTest' computes and returns an empirical p-value from a null distribution generated by permuting 'Dfull' a total of 'num.per' times.

Usage

PermutationTest(Dfull, Dsubsets, num.per, num.chips, alpha)

Arguments

Dfull	dissimilarity matrix from the original (p x n) microarray expression data
Dsubsets	dissimilarity matrices from each k disjoint clusters returned by 'GetClusters'
num.per	number of permutations
num.chips	number of samples, 'n' from the original (p x n) data matrix
alpha	desired level of significance

Details

For each permutation, k Mantel correlations are computed by correlating the permuted 'Dfull' with each dissimilarity matrix 'Dsubsets' from the 'k' clusters returned by 'GetClusters'. The absolute value of the maximum Mantel cluster correlation is retained at each permutation. These 'num.per' maximum correlations are then used to generate a null distribution for distance metric independence, with the p-value taken from the (1 - 'alpha') percentile of this permutation distribution.

Value

returns the permuted p-value for the 'alpha' selected level of significance

Warning

(p x n) data matrix should be numeric (e.g. gene-expression levels)

Note

The function is meant to be executed AFTER 'GetClustes', 'DistMatrices' and 'MantelCorr' (see example)

Author(s)

Brian Steinmeyer

See Also

'GetClusters' 'DistMatrices' 'MantelCorrs'

Examples

# simulate a p x n microarray expression dataset, where p = genes and n = samples
data.sep <- rbind(matrix(rnorm(1000), ncol=50), matrix(rnorm(1000, mean=5), ncol=50))
noise <- matrix(runif(40000), ncol=1000)
data <- t(cbind(data.sep, noise))
data <- data[1:200, ]
# data has p = 1,050 genes and n = 40 samples

clusters.result <- GetClusters(data, 100, 100)
dist.matrices <- DistMatrices(data, clusters.result$clusters)
mantel.corrs <- MantelCorrs(dist.matrices$Dfull, dist.matrices$Dsubsets)
permutation.result <- PermutationTest(dist.matrices$Dfull, dist.matrices$Dsubsets, 100, 40, 0.05)

MantelCorr documentation built on Nov. 8, 2020, 4:58 p.m.