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testing for enrichment of significant individual cpgs #36

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lxw391 opened this issue Feb 24, 2020 · 2 comments
Open

testing for enrichment of significant individual cpgs #36

lxw391 opened this issue Feb 24, 2020 · 2 comments

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@lxw391
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lxw391 commented Feb 24, 2020

Would it be possible to use LOLA to test for enrichment of significant individual CpGs identified in DNA methylation study? we can make a .bed file for each sig CpG, would that be ok to use as input for LOLA? Thanks!
@nsheff
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nsheff commented Feb 24, 2020

You could try it... If there are lots of cpgs it might be slow. You could instead try to group them into regions, that would probably be faster and more accurate. Also consider using the redefineUsersets function to avoid problems with lots of cpgs aligning to the same region in a database.

@lxw391
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lxw391 commented Feb 24, 2020

Great, thanks for the quick reply!

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@nsheff @lxw391