sc-ATAC pro downstream analysis in R

Question

[sidrah.maryam]

During the downstream analysis of the data produced, available on: https://scatacpro-in-r.netlify.app/downstream_in_r In the step TF motif enrichment analysis, the second line :

chromVar.obj = readRDS(paste0(down_dir, '/chromVar_obj.rds'))

this error shows up "Error in if (len > 1) paste(len, " elements, ", sep = "") else "" : argument is of length zero"

Please suggest the reason and a solution for the same. Thanks

[sidrah.maryam]

This protocol

scATAC-pro

Answer 1

[wbaopaul]

I guess you are using an old version of chromVAR package. Update chromVAR should solve your problem.

[sidrah.maryam]

Thank you. It solved the issue.