MantelCorr (version 1.42.0)

MantelCorrs: Compute Mantel Correlation(s)

Description

'MantelCorrs' computes the Mantel correlation between two dissimilarity matrices

Usage

MantelCorrs(Dfull, Dsubsets)

Arguments

Dfull

distance matrix returned by 'DistMatrices' using original 'data'

Dsubsets

list of distance matrices from each k cluster or partition returned by 'DistMatrices'

Value

A list with k components

where component i

Mantel correlation for cluster i, i = 1,...,k

Warning

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

References

Mantel N: The detection of disease clustering and a generalized regression approach. Cancer Research. 27(2), 209-220 (1967).

See Also

'GetClusters' 'DistMatrices' 'kmeans'

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)