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Commit bbe9e867 authored by Laura Denies's avatar Laura Denies
Browse files

Update AMR.R

parent 2a935afa
......@@ -18,6 +18,8 @@ colnames(DeepARG)<- c("DeepARG_ARG","ORF_ID")
# AMR index
PathoFact_AMR_index <- read.delim(file = snakemake@input[["AMR_index"]])
PathoFact_AMR_index$ARG <- toupper(PathoFact_AMR_index$ARG)
PathoFact_AMR_index <- unique(PathoFact_AMR_index)
# Combine
Combined <- full_join(DeepARG, RGI, by="ORF_ID")
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