rnb.execute.clustering {RnBeads} | R Documentation |
Performs hierarchical clustering on the samples of the given dataset using multiple distance metrics and agglomeration methods for a single given region type.
rnb.execute.clustering(rnb.set, region.type = "sites")
rnb.set |
Methylation dataset as an object of type inheriting |
region.type |
the clustering is performed on methylation levels from regions of that type.
see |
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.
Yassen Assenov
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"))