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)[1]
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

Thanks,

Dear Mark,

That is easily solved. The obtained results have the same dimension as the methylation and annotation matrices stored in the rnb.set object. You can access this information using:

anno.genes <- annotation(rnb.set,"genes")
anno.proms <- annotation(rnb.set,"promoters")

This includes all the information you need, like gene symbol, genomic location or Ensembl/Entrez ID. You can obtain the methylation matrix using:

meth.matrix <- meth(rnb.set,"genes/promoters")

Hope that helps!