Extract subset of clusters based on entries in chroms and clusters
Arguments
- treeListClusters
from createClusters()
- clustInclude
data.frame from retainClusters() indcating which clusters to include
Examples
library(GenomicRanges)
library(BiocParallel)
data('decorateData')
# Evaluate hierarchical clustering
treeList = runOrderedClusteringGenome( simData, simLocation )
#>
Evaluating:chr20
#>
# Choose cutoffs and return clusters
treeListClusters = createClusters( treeList )
#> Method:capushe
# Evaluate score for each cluster
clstScore = scoreClusters(treeList, treeListClusters, BPPARAM=SerialParam() )
#> Evaluating strength of each cluster...
#>
#> Dividing work into 1 chunks...
# Retain clusters that pass this criteria
clustInclude = retainClusters( clstScore, "LEF", 0.30 )
#> Using cutoffs:
#> Cluster set cutoff
#> 0.15 0.3
#>
# get retained clusters
treeListClusters_filter = filterClusters( treeListClusters, clustInclude)