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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Bug in runJaccard() #214

Open kridsadakorn opened 3 years ago

kridsadakorn commented 3 years ago

Hi,

Thank you for developing a nice package. I want to try out SnapATAC. I installed the code from Github and I tried to run the demo but it has an error. Do you have any idea why?

> data(demo.sp);
> demo.sp = makeBinary(demo.sp, mat="bmat");
> demo.sp = runJaccard(obj=demo.sp, mat="bmat", bin.downsample=1, tmp.folder=tempdir())
Error in (function (cl, name, valueClass)  : 
  'method' is not a slot in class "jaccard"

Thank you very much.

AndresLugoCas commented 3 years ago

I have the same problem. You were able to fix it?

lf2684 commented 3 years ago

I also encountered this problem--I think after viewing the source code that it's because the jmat class doesn't actually have methods as a slot? I believe the developer posted that runJaccard has actually been discontinued, so I am confused as to how to normalize the data now. For reference: https://github.com/r3fang/SnapATAC/issues/125?fbclid=IwAR13ylSt-UW6dyDZVcWlvTehrdrNob6RsjOzV0ITSOQTGNYN-7002jMEyjo