I'm trying to use
rnbeads to analyse some EPIC methylation arrays. I'm calling the functions individually, rather than running the single report script, so that I have more control over the differential analysis.
I use this code to perform differential methylation and export tables
rnb.set <- rnb.execute.import(data.source = "idats", data.type = "idat.dir") rnb.set.unfiltered <- rnb.set result <- rnb.run.preprocessing(rnb.set.unfiltered, dir.reports=report.dir) rnb.set <- result$rnb.set # Specify the sample annotation table columns for which # differential methylation is to be computed cmp.cols <- "Sample_Group" # Specify the region types reg.types <- c("genes", "promoters") # Conduct the analysis diffmeth <- rnb.execute.computeDiffMeth(rnb.set, cmp.cols, region.types=reg.types) comparison <- get.comparisons(diffmeth) tab.genes <- get.table(diffmeth, comparison, "genes", return.data.frame=TRUE) tab.prom <- get.table(diffmeth, comparison, "promoters", return.data.frame=TRUE) write.csv(tab.genes, file="Genes_Sample_Group.csv",row.names=FALSE) write.csv(tab.prom, file="Promoters_Sample_Group.csv",row.names=FALSE)
However, the resulting tables don't contain any useful identifiers (e.g. gene symbol) only a row number. How can I add annotation to these tables? There must be a function somewhere because the tables generated by the report (which I did run once) had annotation