Commit e166b8b0 authored by Laura Denies's avatar Laura Denies
Browse files

Fix AMR.R error

parent 4280c029
......@@ -23,9 +23,9 @@ PathoFact_AMR_index <- unique(PathoFact_AMR_index)
# Combine
Combined <- full_join(DeepARG, RGI, by="ORF_ID")
Combined$DeepARG_ARG <- fct_explicit_na(Combined$DeepARG_ARG, na_level = "-")
Combined$Best_Hit_ARO <- fct_explicit_na(Combined$Best_Hit_ARO, na_level = "-")
Combined$ARG_SNPs <- fct_explicit_na(Combined$ARG_SNPs, na_level = "n/a")
Combined$DeepARG_ARG <- fct_explicit_na(as.character(Combined$DeepARG_ARG), na_level = "-")
Combined$Best_Hit_ARO <- fct_explicit_na(as.character(Combined$Best_Hit_ARO), na_level = "-")
Combined$ARG_SNPs <- fct_explicit_na(as.character(Combined$ARG_SNPs), na_level = "n/a")
Combined$Best_Hit_ARO <- toupper(Combined$Best_Hit_ARO)
Unique <- Combined %>% filter(Combined$DeepARG_ARG == "-" | Combined$Best_Hit_ARO == "-")
......
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