MantelCorrs: Compute Mantel Correlation(s)

In MantelCorr: Compute Mantel Cluster Correlations

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)

Note

the value 'k' corresponds to the parameter 'num.k' in 'GetClusters'

Author(s)

Brian Steinmeyer

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)

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