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Durenlab / RegNMF

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cis-regulatory score #3

Open lebf3 opened 2 years ago

lebf3 commented 2 years ago

Hi, I would like to have some details on the CRS output. In your paper you mention ; higher CRS in a subpopulation indicates a potential cis-regulation

But the output from SplitGroup are the 10000 RE-TG pairs with lowest CRS values for that cell type. https://github.com/Durenlab/RegNMF/blob/3a2efd190c73a78d920b42baf8a4e7074e582b64/R/SplitGroup.default.R#L39

From what I understand, a higher cell-level cis-regulatory potential Rijc should indicate stronger effect. Can you clarify why the output are sorted for lowest 10000 values?

Thanks, Francis

lebf3 commented 2 years ago

Also, the ATACseq data seem to be log10 transformed while the RNAseq data is log2 transformed https://github.com/Durenlab/RegNMF/blob/3a2efd190c73a78d920b42baf8a4e7074e582b64/R/read_ATAC_GEX.default.R#L56