Find which cluster a peak is in

Find which cluster a peak is in

Usage

whichCluster(treeListClusters, feature_id, id = NULL)

Arguments

treeListClusters

from createClusters()

feature_id

name of query feature, can also be array

id

clustering parameter identifier. After filtering by feature_id, filter by id

Value

data.frame of chromosome and cluster

Examples

library(GenomicRanges)

data('decorateData')

# Evaluate hierarchical clustering
treeList = runOrderedClusteringGenome( simData, simLocation ) 
#> 
Evaluating:chr20          
#> 

# Choose cutoffs and return clusters
treeListClusters = createClusters( treeList, method='meanClusterSize', meanClusterSize = c(50, 100) )
#> Method:meanClusterSize

# Find chromsome and cluster of peak_20
whichCluster( treeListClusters, 'peak_20')
#>    id chrom feature_id cluster
#> 1  50 chr20    peak_20       1
#> 2 100 chr20    peak_20       1

# Find chromsome and cluster of peak_20 with clustering parameter 50 
#  corresponding to meanClusterSize 
whichCluster( treeListClusters, 'peak_20', "50")
#>   id chrom feature_id cluster
#> 1 50 chr20    peak_20       1

# Search for multiple clusters
whichCluster( treeListClusters, c('peak_20', 'peak_21'), "50")
#>   id chrom feature_id cluster
#> 1 50 chr20    peak_20       1
#> 2 50 chr20    peak_21       1