CHANGES IN DMRcate VERSION 1.0.2 BUG FIXES • annotate() renamed to cpg.annotate to avoid clashes with same-named function in ggplot2 NEW FEATURES • Kernel estimator has been rewritten from scratch without the need for ks:::kde. Now only takes moderated t-values as cpg weights, as required by the chi-square transformation. • Now allows for multi-level factor experiments, as allowed by limma. Contrasts should be specified with a contrast matrix, otherwise the design matrix MUST have an intercept. (Thanks to Tim Triche Jr. and David Martino for their advice). • A GRanges object can be produced from the results. • XY probes can also be filtered out using rmSNPandCH(). • DMR.plot() allows group median lines to be plotted to better visualise distances between groups (Thanks to Susan van Dijk and Magnus Tobiasson for their advice).