differential methylation analysis with RnBeads
Entering edit mode
Last seen 4.6 years ago

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)

rnbeads methylation methylationepic dna methylation • 620 views

Login before adding your answer.

Traffic: 405 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6