Find Modules with Hierarchical Clustering

This function finds modules from Hierarchical Clustering `fastcluster::hclust.vector()`

Usage

findModules.hclust(
  adj,
  aggloMethod = "ward",
  clustDistance = "euclidean",
  minModuleSize = 30
)

Arguments

adj

Required. A n x n upper triangular adjacency in the matrix class format.

aggloMethod

Optional. The agglomeration method to be used. This must be (an unambiguous abbreviation of) one of "single", "ward", "centroid" or "median". (Default = "ward")

clustDistance

Optional. The distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Any unambiguous substring can be given. (Default = "euclidean")

minModuleSize

Optional. Integer between 1 and n genes. (Default = 30)

Value

GeneModules = n x 3 dimensional data frame with column names as Gene.ID, moduleNumber, and moduleLabel.