I am analyzing a MethylationEPIC beadchip from Illumina with the RnBeads package. Everything looks fine but the final result (differential methylation analysis between groups) does not generate a report (html or pdf). What might be the error here?
#set up analysis environment
> data.dir <- "folder"
> idat.dir <- file.path(data.dir, "idat_folder")
> sample.annotation <- file.path(data.dir, "annotation.csv")
> analysis.dir <- "~/RnBeads/analysis"
> report.dir <- file.path(analysis.dir, "reports")
#load samples and annotation
> data.source <- c(idat.dir, sample.annotation)
> result <- rnb.run.import(data.source=data.source, data.type="infinium.idat.dir", dir.reports=report.dir)
> rnb.set <- result$rnb.set
#run quality control analysis
> rnb.run.qc(rnb.set, report.dir)
#run preprocessing of data
> rnb.set.unfiltered <- rnb.set
> result <- rnb.run.preprocessing(rnb.set.unfiltered, dir.reports=report.dir)
> rnb.set <- result$rnb.set
#differential methylation analysis (non-adjusted)
> cmp.cols <- “Sample_Group”
> reg.types <- c(“genes”, “promoters”, “tiling”, “cpgislands”)
> diffmeth <- rnb.execute.computeDiffMeth(rnb.set, cmp.cols, region.types=reg.types)