Figure 2
Tuning of the of d min and n min parameters. (A) Number of regions identified and (B) fraction of all probes included in these regions using different settings of dmin and nmin. dmin denotes the maximal distance in bp allowed between two adjacent probes to be accepted in the same region. nmin denotes the minimal number of probes in a region (per sample). All runs of the algorithm were done using the 415,712 probes annotated to at least one Illumina class grouped according to gene/transcription start site/CpG island (recode parameter = 1). These benchmark statistics can be generated using the tune_parameters function in the algorithm (optional parallelization).