Question: How to do DMR analysis with BiSeq (for RRBS methylation data)?
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gravatar for ahmad.moousavi
16 days ago by
Royan Institute, Tehran, Iran
ahmad.moousavi40 wrote:

Hi

I have 20 RRBS samples which I wanted to do do deferentially methylated region (DMR) analysis with BiSeq or other R packages, however the manual resource is not enough. I want to do DMR analysis on all chromosomes not specific regions.

Is there anybody who has experience with BiSeq:

> readBismark(files, colData)
> metadata <- list(Sequencer = "Instrument", Year = "2013")
> rowRanges <- GRanges(seqnames = "chr1",ranges = IRanges(start = c(1,2,3), end = c(1,2,3)))
> colData <- DataFrame(group = c("cancer", "control"), row.names = c("sample_1", "sample_2"))
> totalReads <- matrix(c(rep(10L, 3), rep(5L, 3)), ncol = 2)
> methReads <- matrix(c(rep(5L, 3), rep(5L, 3)), ncol = 2)
> BSraw(metadata = metadata,rowRanges = rowRanges,colData = colData,totalReads = totalReads,methReads = methReads)
sequencing dmr methylation • 131 views
ADD COMMENTlink modified 16 days ago • written 16 days ago by ahmad.moousavi40

This does not answer your BiSeq question directly, but I've been very happy using metilene for DMR calling.

ADD REPLYlink written 16 days ago by Chris Miller19k
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