createClusters: Create cluster from list of hclust objects

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Create cluster from list of hclust objects

Description

Create cluster from list of hclust objects

Usage

createClusters(
  treeList,
  method = c("capushe", "bstick", "meanClusterSize"),
  meanClusterSize = 50,
  pct = 0.15
)

Arguments

treeList	list of hclust objects
method	'capushe': slope heuristic. 'bstick': broken stick. 'meanClusterSize': create clusters based on target mean value.
meanClusterSize	select target mean cluster size. Can be an array of values
pct	minimum percentage of points for the plateau selection in capushe selection. Can be an array of values

Value

Convert hierarchical clustering into discrete clusters based on selection criteria method

Examples

library(GenomicRanges)
library(EnsDb.Hsapiens.v86)

# load data
data('decorateData')

# load gene locations
ensdb = EnsDb.Hsapiens.v86

# Evaluate hierarchical clustering
treeList = runOrderedClusteringGenome( simData, simLocation ) 

# Choose cutoffs and return clusters
treeListClusters = createClusters( treeList )

# Plot correlations and clusters in region defined by query
query = range(simLocation)

plotDecorate( ensdb, treeList, treeListClusters, simLocation, query)

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.