RnBeads (version 1.4.0)

rnb.execute.clustering: rnb.execute.clustering

Description

Performs hierarchical clustering on the samples of the given dataset using multiple distance metrics and agglomeration methods for a single given region type.

Usage

rnb.execute.clustering(rnb.set, region.type = "sites")

Arguments

rnb.set

Methylation dataset as an object of type inheriting RnBSet.

region.type

the clustering is performed on methylation levels from regions of that type. see rnb.region.types for possible values.

Value

List of clustering results, whereby each element is an object of type RnBeadClustering. In case clustering cannot be performed, the return value is NULL. Reasons for a failure include, among others, the case when rnb.set contains less than 3 samples, or undefined distances between a pair of samples due to (too many) missing values in the respective methylation matrix.

Examples

library(RnBeads.hg19)
data(small.example.object)
results <- rnb.execute.clustering(rnb.set.example, "promoters")
# List applied dissimilarity metrics
sapply(results, slot, "dissimilarity")
# List applied clustering algorithms
str(lapply(results, slot, "algorithm"))