Collapse clusters if jaccard index between clusters exceeds a cutoff
Arguments
- treeListClusters
from createClusters()
- featurePositions
GRanges object storing location of each feature
- jaccardCutoff
cutoff value for jaccard index
Examples
library(GenomicRanges)
#> Loading required package: stats4
#> Loading required package: S4Vectors
#>
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#>
#> findMatches
#> The following objects are masked from ‘package:base’:
#>
#> I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
library(BiocParallel)
# load data
data('decorateData')
# Evaluate hierarchical clustering
# adjacentCount is the number of adjacent peaks considered in correlation
treeList = runOrderedClusteringGenome( simData, simLocation)
#>
Evaluating:chr20
#>
# Choose cutoffs and return cluster
treeListClusters = createClusters( treeList, method = "meanClusterSize", meanClusterSize=c( 10, 20, 30, 40, 50) )
#> Method:meanClusterSize
# Evaluate strength of correlation for each cluster
clstScore = scoreClusters(treeList, treeListClusters, BPPARAM = SerialParam() )
#> Evaluating strength of each cluster...
#>
#> Dividing work into 5 chunks...
# Filter to retain only strong clusters
clustInclude = retainClusters( clstScore, "LEF", 0.30 )
#> Using cutoffs:
#> Cluster set cutoff
#> 10 0.3
#> 20 0.3
#> 30 0.3
#> 40 0.3
#> 50 0.3
#>
# get retained clusters
treeListClusters_filter = filterClusters( treeListClusters, clustInclude)
# collapse similar clusters
treeListClusters_collapse = collapseClusters( treeListClusters_filter, simLocation)
#> Identifying redundant clusters...