MantelCorrs {MantelCorr} | R Documentation |
'MantelCorrs' computes the Mantel correlation between two dissimilarity matrices
MantelCorrs(Dfull, Dsubsets)
Dfull |
distance matrix returned by 'DistMatrices' using original 'data' |
Dsubsets |
list of distance matrices from each k cluster or partition returned by 'DistMatrices' |
A list with k components
where component i |
Mantel correlation for cluster i, i = 1,...,k |
The function is meant to be executed AFTER 'GetClustes' and 'DistMatrices' (see example)
the value 'k' corresponds to the parameter 'num.k' in 'GetClusters'
Brian Steinmeyer
Mantel N: The detection of disease clustering and a generalized regression approach. Cancer Research. 27(2), 209-220 (1967).
'GetClusters' 'DistMatrices' 'kmeans'
# 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)