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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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Add covariates to the model #18

Closed csijcs closed 2 years ago

csijcs commented 3 years ago

Really great tool.

Is it possible to add a covariate to the model? Specifically I would like to add copy number as a covariate rather than make a cutoff and blacklist regions. Is there a simple way to do this?

Thanks so much

ay-lab commented 3 years ago

Hi, Thanks for using the tool. This is a very interesting question but will require some extensive study. Have you just tried to simply normalize the counts based on their copy numbers and perform the dchic? https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2256-5

csijcs commented 3 years ago

Thanks for the reply. I have used that methodology for CNV normalisation, but it works in conjunction with the iterative correction. So the resulting matrices are both ICE normalised and CNV normalized, and I thought for your methodology the input needed to be the raw matrices. If its ok to use ICE normalised matrices with dchic then I can give it a try.