runOrderedClustering: Run hierarchical clustering preserving order

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Run hierarchical clustering preserving order

Description

Run hierarchical clustering preserving sequential order of entries

Usage

runOrderedClustering(X, gr, alpha = 0.5)

Arguments

X	data matrix were *rows* are features in sequential order
gr	GenomicRanges object corresponding to rows in X
alpha	mixture parameter weigting correlations (alpha=0) versus chromosome distances (alpha=1)

Details

Use hclustgeo in ClustGeo package to generate hierarchical clustering that preserves sequential order.

Chavent, et al. 2017. ClustGeo: an R package for hierarchical clustering with spatial constraints. arXiv:1707.03897v2 doi:10.1007/s00180-018-0791-1

Value

hclust tree

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.