Check results returned with and without tumor type parameter and document differences

[karissawhiting]

When you run the functions with and without the tumor type parameter you get different columns of data back. This is to be expected but we should double check data is consistent between them and also check and document what is being returned in each.

We may want to add some info/warning messages accordingly.

library(oncokbR)
library(dplyr)

blca_mutation <- oncokbR::blca_mutation %>%
  mutate(tumor_type = "BLCA")

annotated_with_type <- annotate_mutations(mutations = blca_mutation[1:50,])

blca_mutation <- oncokbR::blca_mutation

annotated_no_type <- annotate_mutations(mutations = blca_mutation[1:50,])

annotated_no_type %>%
  select(oncogenic) %>% 
  table()

[karissawhiting]

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