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Get feature names in selected cluster given array of chrom and cluster ids

Usage

getFeaturesInClusterList(treeListClusters, chrom, clustID, id)

Arguments

treeListClusters

from createClusters()

chrom

chromosome name of cluster

clustID

cluster identifier

id

clustering parameter identifier

Value

list of array of feature names. Query with index i as returned in list index i

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 = 50 )
#> Method:meanClusterSize

df_cluster = data.frame( chrom = c("chr20", "chr20"), 
  cluster = c(3,5), 
  id = c("50", "50"), stringsAsFactors=FALSE )

# Find features for the clusters in df_cluster
getFeaturesInClusterList( treeListClusters, chrom=df_cluster$chrom, clustID=df_cluster$cluster, id=df_cluster$id)
#> [[1]]
#>  [1] "peak_100" "peak_101" "peak_102" "peak_103" "peak_104" "peak_105"
#>  [7] "peak_106" "peak_107" "peak_108" "peak_109" "peak_110" "peak_111"
#> [13] "peak_112" "peak_113" "peak_114" "peak_115" "peak_116" "peak_117"
#> [19] "peak_118" "peak_119" "peak_120" "peak_121" "peak_122" "peak_123"
#> [25] "peak_124" "peak_125"
#> 
#> [[2]]
#>  [1] "peak_183" "peak_184" "peak_185" "peak_186" "peak_187" "peak_188"
#>  [7] "peak_189" "peak_190" "peak_191" "peak_192" "peak_193" "peak_194"
#> [13] "peak_195" "peak_196" "peak_197" "peak_198" "peak_199" "peak_200"
#> [19] "peak_201" "peak_202" "peak_203" "peak_204" "peak_205" "peak_206"
#> [25] "peak_207" "peak_208" "peak_209" "peak_210" "peak_211" "peak_212"
#> [31] "peak_213" "peak_214" "peak_215" "peak_216" "peak_217" "peak_218"
#> [37] "peak_219" "peak_220" "peak_221" "peak_222" "peak_223" "peak_224"
#> [43] "peak_225" "peak_226" "peak_227" "peak_228" "peak_229" "peak_230"
#> [49] "peak_231" "peak_232" "peak_233" "peak_234" "peak_235" "peak_236"
#> [55] "peak_237" "peak_238" "peak_239" "peak_240"
#>