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In particular, statistical identification of differentially methylated regions across different conditions poses unresolved challenges in accounting for spatial correlations within the statistical testing procedure.<\/jats:p><jats:p>Results: We propose a non-parametric, kernel-based method, M3D, to detect higher order changes in methylation profiles, such as shape, across pre-defined regions. The test statistic explicitly accounts for differences in coverage levels between samples, thus handling in a principled way a major confounder in the analysis of methylation data. Empirical tests on real and simulated datasets show an increased power compared to established methods, as well as considerable robustness with respect to coverage and replication levels.<\/jats:p><jats:p>Availability and implementation: R\/Bioconductor package M3D.<\/jats:p><jats:p>Contact: \u00a0G.Sanguinetti@ed.ac.uk<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu749","type":"journal-article","created":{"date-parts":[[2014,11,15]],"date-time":"2014-11-15T04:10:48Z","timestamp":1416024648000},"page":"809-816","source":"Crossref","is-referenced-by-count":29,"title":["M3D: a kernel-based test for spatially correlated changes in methylation profiles"],"prefix":"10.1093","volume":"31","author":[{"given":"Tom R.","family":"Mayo","sequence":"first","affiliation":[{"name":"1 IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and 2Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gabriele","family":"Schweikert","sequence":"additional","affiliation":[{"name":"1 IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and 2Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK"},{"name":"1 IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and 2Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guido","family":"Sanguinetti","sequence":"additional","affiliation":[{"name":"1 IANC, School of Informatics, University of Edinburgh, Edinburgh EH8 9AB and 2Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,11,13]]},"reference":[{"key":"2023020116180496600_btu749-B1","doi-asserted-by":"crossref","first-page":"1650","DOI":"10.1093\/bioinformatics\/btn250","article-title":"Ontologizer 2.0a multifunctional tool for go term enrichment analysis and data exploration","volume":"24","author":"Bauer","year":"2008","journal-title":"Bioinformatics"},{"key":"2023020116180496600_btu749-B2","doi-asserted-by":"crossref","first-page":"698","DOI":"10.4161\/epi.28322","article-title":"Magi: methylation analysis using genome information","volume":"9","author":"Baumann","year":"2014","journal-title":"Epigenetics"},{"key":"2023020116180496600_btu749-B3","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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