runOrderedClustering: Run hierarchical clustering preserving order

Description Usage Arguments Details Value Examples

View source: R/local_correlations.R

Description

Run hierarchical clustering preserving sequential order of entries

Usage

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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

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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 Aug. 8, 2019, 1:48 p.m.