Run hierarchical clustering preserving order — runOrderedClustering • decorate

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)

Value

hclust tree

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

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 ) 
#> 
Evaluating:chr20          
#> 

# Choose cutoffs and return clusters
treeListClusters = createClusters( treeList )
#> Method:capushe

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

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