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This is not currently supported in the software |
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Can you use ClosestFeature and then just summarize by feature? |
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Hello. This may be a very basic question, so thank you in advance for helping me understand and find a solution to my problem. I would like to create a new gene activity assay derived from scATAC-seq data, but rather than summing the fragments intersecting the gene body and promoter region (as GeneActivity() does), I would like to assign all the fragments to the nearest gene body, regardless of their distance to it. Is there a way to change the parameters used to assign fragments to genes in the GeneActivity() function beyond just changing how far the promoter region should extend upstream?
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