ks parameter input missing in association and association.Seurat functions

[shobhitagrawal1]

Hi,
Thanks for developing and maitaining an R version of the package. Really interesting method!
In the rcna package:

1. I frequently get this warning:
   " In .association(NAMsvd = list(nam_res$NAM_sampleXpc, nam_res$NAM_svs, :
   data supported use of 5 NAM PCs, which is the maximum considered. Consider allowing more PCs by using the "ks" argument."
   I could subset my data and maybe then 5NAM PCs would be enough but it would be nice to be allowed to test the functions with greater ks.
   I ran through the raw code on github and there is no provision of input for the ks parameter both in the association and association.Seurat function.
2. Is there a way to extract the neighborhoods and cells belonging to a particular neighborhood ?
   Thank you very much,
   shobhit

[christensensm]

I'm getting the same message from 1 and would like to allow more PCs! Has this been addressed yet?

Also curious about the second question.

[shobhitagrawal1]

Hey, this was a long ago. But in general, my tips would be:

1. Data subsetting
2. Make sure that variables you are interested in are numeric factors (and not characters by any chance). And the levels make sense in case you subset the data.
   -- although it works for me, the code, one has to be aware that there was an error found in the original python rep. Not sure how this affects the R repo.