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. 2014 May 15;15:141. doi: 10.1186/1471-2105-15-141

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Copyright © 2014 Rijlaarsdam et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Tuning of the of d_minand n_minparameters. (A) Number of regions identified and (B) fraction of all probes included in these regions using different settings of d_min and n_min. d_min denotes the maximal distance in bp allowed between two adjacent probes to be accepted in the same region. n_min 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).