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kaizhang / SnapATAC2

Single-cell epigenomics analysis tools
https://kzhang.org/SnapATAC2/
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Question about differential test #340

Closed beyondpie closed 1 month ago

beyondpie commented 1 month ago

Hi Kai, From the codes below, https://github.com/kaizhang/SnapATAC2/blob/942f056a9c7612eb06db1d2596eb89475a0fb818/snapatac2-python/python/snapatac2/tools/_diff.py#L128 it seems that current diff_test does not accept covariates? If I want to get cell-type specific peaks, what will the null model be? A logistic regression without any features except a 1 ?

Thanks! Songpeng

kaizhang commented 1 month ago

Use cell_group1 and cell_group2 to compare two cell groups at a time. covariates current is not implemented. It is used to regress out additional cofounding factors. It is easy to add.