Hi,
I was just wondering if the difference between the two available GRCh38 reference files could be clarified. These are RefCDS_human_GRCh38.p12_dNdScv.0.1.0.rda and RefCDS_human_GRCh38_GencodeV18_recommended.rda. I have run dndscv with both of these and the former hits an error only when using the covariate data, while the latter runs smoothly when using the covariate data. I see that Gencode V18 was GRCh37.p12. Was this lifted over to GRCh38?
I have added the function call and error below for reference:
load("covariates_hg19_hg38_epigenome_pcawg.rda")
dndscv(mutations = mdata, refdb = 'RefCDS_human_GRCh38.p12_dNdScv.0.1.0.rda',cv = covs)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': subscript out of bounds
Thank you!
Hi,
I was just wondering if the difference between the two available GRCh38 reference files could be clarified. These are RefCDS_human_GRCh38.p12_dNdScv.0.1.0.rda and RefCDS_human_GRCh38_GencodeV18_recommended.rda. I have run dndscv with both of these and the former hits an error only when using the covariate data, while the latter runs smoothly when using the covariate data. I see that Gencode V18 was GRCh37.p12. Was this lifted over to GRCh38?
I have added the function call and error below for reference:
load("covariates_hg19_hg38_epigenome_pcawg.rda")
dndscv(mutations = mdata, refdb = 'RefCDS_human_GRCh38.p12_dNdScv.0.1.0.rda',cv = covs)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.matrix': subscript out of bounds
Thank you!