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Question: differential methylation analysis with RnBeads
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gravatar for gabrielrfries
7 months ago by
gabrielrfries0 wrote:

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)

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