I would like to manually extract differential methylation data tables from RnBDiffMeth object. By the "data table" I mean a table in which I have both genomic region annotations and corresponding methylation statistics (such tables are normally attached in report generated by rnb.run.differential function).
I have created RnBDiffMeth object using command:
regions <- rnb.execute.computeDiffMeth( x = Inference_result$rnb.set, pheno.cols = c("i_vs_c", "b_vs_rest", "b_vs_c", "i_vs_rest", "e_vs_c"), region.types = c("tiling", "cpgislands", "genes", "promoters", "tiling200bp") columns.adj = rnb.getOption("covariate.adjustment.columns"), adjust.sva = rnb.getOption("differential.adjustment.sva"), pheno.cols.adjust.sva = rnb.getOption("inference.targets.sva"))
To extract data tables from this object, I have tried functions exportDMRs2regionFile (which does not generate statistical data) and get.table (which, as far as I see, has only "orphaned" statistics, with no key which would allow me to match these statistics to corresponding genomic region). Is there a way to annotate get.table with genomic data?
I am doing this as a way to learn the RnBeads package to find a solution or workaround for another issue Im having.