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dozmorovlab / TADCompare

Package for analysis and characterization of differential TADs
https://dozmorovlab.github.io/TADCompare/
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How to use TADCompare with output of ConsensusTADs? #5

Closed srcoulombe closed 4 years ago

srcoulombe commented 4 years ago

I'm struggling to understand how the output of ConsensusTADs could be used as input to TADCompare. From what I understand, the All_Regions dataframe returned by ConsensusTADs could theoretically be substituted in place of point_dists# in TADCompare.R, but that's not built-in. I'm also not sure I understand whyTADCompare's pre_tads kwarg needs paired boundary coordinates. Is there any chance that TADCompare will eventually be able to use the outcome of ConsensusTADs to do group-vs-group comparisons? Or is there something I'm missing or misunderstanding?

srcoulombe commented 4 years ago

Aaah wait sorry I think what I'm trying to do could be done outside of TADCompare by just applying the z-test to the two concensus tracks. Sorry for raising the issue, I think I've got it from here.