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CostaLab / scMEGA

scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
https://costalab.github.io/scMEGA
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snATAC data does not have a $Harmony dimension reduced matrix #13

Closed liyang24 closed 1 year ago

liyang24 commented 1 year ago

Hi! I noticed that I needed to use $Harmony in the tutorial to prepare the data

add dimension reduced matrix

harmony_matDR <- proj@reducedDims$Harmony$matDR

but I only had $UMAP in my data ,because my samples are not duplicated. In this case, can I still use this tutorial? How can I get the final obj.atac?

lzj1769 commented 1 year ago

Sure, you can use the UMAP embedding.