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al2na / methylKit

R package for DNA methylation analysis
https://bioconductor.org/packages/release/bioc/html/methylKit.html
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How to use methyKit with two platform data with different coverage distribution #260

Open liuyangzzu opened 2 years ago

liuyangzzu commented 2 years ago

Dear author,

I have two platform generated methylation data. The coverage of Platform1 is very high >25x, however, Platform2's data coverage is very low ~3-5x.

Each platform I have one sample in ctrl and one sample in test group.

I want to call DMC in each platform ctrl/test group, and compare the called CpGs between the two platform. In this case, can I directly use the Fisher test in methyKit, no matter the coverage difference of the two platform? Thank you for your help!

Best, Yang

alexg9010 commented 2 years ago

Hi @liuyangzzu,

In general, when processing methylation data, we advise a minimum coverage threshold of 10 reads per base, thus many sites from your second platform's data may already be filtered out. IMHO, given this strong difference in coverage, it would not be reasonable to perform the logistic regression-based tests.

To answer your question, when there is only one sample per sample group, calculateDiffMeth() automatically applies Fisher’s exact test.

Best Alex

al2na commented 1 year ago

Yes, you can !! Please update us about the results. This is very interesting, would be good to know how concordant Rrbs and ONT

On Thu, Jul 7, 2022 at 9:53 PM Yang Liu @.***> wrote:

Dear author,

I have two platform generated data, RRBS and ONT. The coverage of RRBS is very high >25x, however, ONT data coverage is very low ~3-5x.

Each platform I have one sample in ctrl and one sample in test group.

I want to call DMC in each platform ctrl/test group, and compare the CpG difference between the two platform. In this case, can I directly use the Fisher test in methyKit, no matter the coverage difference of the two platform? Thank you for your help!

Best, Yang

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