ClusterList {MantelCorr} | R Documentation |
'ClusterList' generates a list of both significant and nonsignificant clusters, with cluster number, Mantel cluster correlation and size
ClusterList(p.val, clus.size, mantel.cors)
p.val |
permutation p-value returned from 'PermutationTest' |
clus.size |
vector of k cluster sizes returned from 'GetCluster' |
mantel.cors |
orignal, unpermuted k Mantel correlations returned from 'MantelCorrs' |
A list with components:
SignificantClusters |
clusters with significant Mantel correlation, equal to or larger than the permutation p-value returned by 'PermutationTest' |
NonSignificantClusters |
clusters with nonsignificant Mantel correlation, smaller than the permutation p-value returned by 'PermutationTest' |
Brian Steinmeyer
'PermutationTest'
# 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$Dsubsets, 100, 40, 0.05) # generate both significant and non-significant gene clusters cluster.list <- ClusterList(permutation.result, clusters.result$cluster.sizes, mantel.corrs)