Closed SamakshSingh99 closed 9 months ago
Hi,
For the 1st error you can connect to the ensembl Marts before running the pipeline and explicitly give the objects to _vargenpipeline like so:
gene_mart <- connect_to_gene_ensembl("useast")
snp_mart <- connect_to_snp_ensembl("useast")
obesity_variants <- vargen_pipeline(vargen_dir = "./vargen_data/",
omim_morbid_ids = "601665",
gtex_tissues = adipose_tissues,
gwas_traits = obesity_traits,
gene_mart = gene_mart,
snp_mart = snp_mart,
verbose = T)
For the 2nd error, the latest commits should have fixed it, please remove the vargen package from your R environnement, restart R, then reinstall the vargen package. And you will need to run _vargeninstall again, as this will download _enhancer_tssassociations.bed:
vargen_install(install_dir = "./vargen_data", gtex_version = "v8", verbose = T)
Let me know if this solution worked.
Hi! On trying to run the VarGen pipeline as mentioned in the tutorial I am coming across two different error on running it two different times mentioned as follows:
Error_1
Error_2