When mutations are pulled via API, the name of the variant classification column is mutationType. Could clarify error messaging to say variant_classification or mutationType column not found.
Error in sanitize_mutation_input() at gnomeR/R/create-gene-binary.R:142:2:
! No variant_classification column found therefore silent mutations can't be removed. Please set
include_silent = TRUE or add a variant_classification column.
Discussed with @karissawhiting on 5/11/2023. Encountered this in the following scenario: when I run create_gene_binary() on the mutations file i pulled from the portal, it runs fine. when i run oncokb annotations and then try to run create gene binary again, i get an error that the variant classification column isn't found so it can't remove silent mutations. but when i look at the not oncokb annotated mutations file, there isn't a variant_classification variable there either, so i'm not sure what is changing after the annotation that it's throwing the error.
When mutations are pulled via API, the name of the variant classification column is mutationType. Could clarify error messaging to say variant_classification or mutationType column not found.
Error in
sanitize_mutation_input()at gnomeR/R/create-gene-binary.R:142:2: ! Novariant_classificationcolumn found therefore silent mutations can't be removed. Please setinclude_silent = TRUEor add avariant_classificationcolumn.Discussed with @karissawhiting on 5/11/2023. Encountered this in the following scenario: when I run
create_gene_binary()on the mutations file i pulled from the portal, it runs fine. when i run oncokb annotations and then try to run create gene binary again, i get an error that the variant classification column isn't found so it can't remove silent mutations. but when i look at the not oncokb annotated mutations file, there isn't a variant_classification variable there either, so i'm not sure what is changing after the annotation that it's throwing the error.