using which refCDS-hg38? doubt for covariate
complexgenome opened this issue · 1 comments
complexgenome commented
Hello there,
Hope this finds you well. Thank you for this tool.
I've Whole-exome data, hg38 human genome build. I downloaded data from https://github.com/im3sanger/dndscv_data/tree/master/data
I use the following code to have a first run:
dndsout = dndscv(df_mutation, refdb="RefCDS_human_GRCh38_GencodeV18_recommended.rda", cv=NULL)
print(dndsout$sel_cv)
It works and no issues.
I've some questions on using files with covariates.
What covariates do I provide when I use RefCDS_human_hg19_GencodeV18_newcovariates.rda file? Or do I provide cv=null when using this file?
There are no covariates for hg38 in the data shipped with library.
Sorry, the manual doesn't mention much on this. https://htmlpreview.github.io/?http://github.com/im3sanger/dndscv/blob/master/vignettes/buildref.html
Looking forward for your inputs.
im3sanger commented