Quantify variance explained by individual factors on the Principle components.

[annrosebright]

Hi,

I have different stage-specific scATACseq datasets. An analysis I would like to perform is to quantify the variance by factors ( distal peak, promoters. gene bodies) on the various PC components. How much variance does the first PC explain? Is there a way to extract this information?
Sorry if I have not explained it well.
Thanks in advance.

[rcorces]

In scATAC, we dont have PCs per se. LSI and SVD are slightly different, but you can obtain variance explained by the various singular values of SVD. I do not have code to do this but google may help.