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Ed Schwalbe
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20
@ed-schwalbe-5262
Last seen 10.2 years ago
Dear List,
I have preprocessed my 450k methylation array data using minfi and
have identified differentially methylated probes in my cancer dataset.
I would like to take advantage of the nice position-dependent/gene-
focussed methylation heatmaps available in the methyAnalysis package
but am unsure as to how to coerce from a minfi Methylset (or a
GenomicMethylSet, which might be more appropriate) into the
MethyGenoSet class used by MethyAnalysis.
Is there any way to do this?
Oh, and as an aside, is there any progress on directly applying the
bumphunter algorithm to the 450k data? I've never managed to find any
DMRs using the dmrFinder function in the CHARM package (function
reports zero DMRs), so I must be doing something wrong, as I'm sure
that they are present within my dataset.
Thanks,
Ed
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