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smithlabcode / dnmtools

Tools for analyzing DNA methylation data
https://dnmtools.readthedocs.io
GNU General Public License v3.0
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P value in diff and dmr #250

Closed JJJelly77 closed 1 week ago

JJJelly77 commented 2 weeks ago

Hello ! Thank you for the fast and convenient dnmtools I want to output p value when running diff and dmr, but I don't find any parameters that can be used.

I hope you can see this problem and look forward to your reply

andrewdavidsmith commented 2 weeks ago

Sure, I'll have a look. Can you provide the command line you've been using?

JJJelly77 commented 2 weeks ago

Thank you for your prompt reply！ I want to calculate differential methylation sites and regions separately, and I would love to know the P-value for each site and region, here is my command：

dnmtools diff -o hols_leiq.diff holstein.v1.meth leiqiong.v1.meth

dnmtools dmr hols_leiq.diff holstein.hmr leiqiong.hmr dmr.hols.bed dmr.leiq.bed

How do I get the P values included in the output file

andrewdavidsmith commented 1 week ago

Which p values? There is no p-value for the intervals that differs from the collection of p-values within the input, and there would be no way to have a structured representation that combines them because it's many-to-1.

JJJelly77 commented 1 week ago

I understand what you mean now, thank you for your explanation