filterClusters: Extract subset of clusters

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Extract subset of clusters

Description

Extract subset of clusters based on entries in chroms and clusters

Usage

filterClusters(treeListClusters, clustInclude)

Arguments

treeListClusters	from createClusters()
clustInclude	data.frame from retainClusters() indcating which clusters to include

Value

epiclustDiscreteList of specified clusters

Examples

library(GenomicRanges)
library(BiocParallel)

data('decorateData')

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

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

# Evaluate score for each cluster
clstScore = scoreClusters(treeList, treeListClusters, BPPARAM=SerialParam() )

# Retain clusters that pass this criteria
clustInclude = retainClusters( clstScore, "LEF", 0.30 )

# get retained clusters
treeListClusters_filter = filterClusters( treeListClusters, clustInclude)

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