ClusterList: Generate a Cluster List

Description Usage Arguments Value Author(s) See Also Examples

View source: R/ClusterList.r

Description

'ClusterList' generates a list of both significant and nonsignificant clusters, with cluster number, Mantel cluster correlation and size

Usage

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ClusterList(p.val, clus.size, mantel.cors)

Arguments

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'

Value

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'

Author(s)

Brian Steinmeyer

See Also

'PermutationTest'

Examples

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# 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)

MantelCorr documentation built on May 2, 2018, 2:46 a.m.