Get genome coordinates for each cluster — getClusterRanges • decorate

Get genome coordinates for each cluster as a GRanges object

Usage

getClusterRanges(gRanges, clustList, verbose = TRUE)

Arguments

gRanges: GenomciRanges corresponding to the rows of epiSignal
clustList: list of cluster assignments
verbose: write messages to screen

Value

GRanges object

Examples

library(GenomicRanges)

# 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

# Get start and end coordinates for each cluster
# cluster name is parameter:chrom:cluster
getClusterRanges( simLocation, treeListClusters)
#> Summarizing each cluster...