Commit 1fe55556 authored by Laura Denies's avatar Laura Denies
Browse files

Updated AMR_MGE.R

parent aacfeddb
......@@ -71,6 +71,10 @@ colnames(VirSorter)<- c("ContigID","VirSorter_prediction")
VirSorter$ContigID <- as.numeric(as.character(VirSorter$ContigID))
VirSorter$ContigID <- sprintf("%010d", VirSorter$ContigID)
## Combine Phage prediction
Phage_prediction <- merge(VirFinder, VirSorter, by="ContigID", all = TRUE)
Phage_prediction$VirSorter_prediction <- fct_explicit_na(Phage_prediction$VirSorter_prediction, na_level = "-")
# Combine AMR/MGE with Phage prediction
AMR_MGE <- merge(AMR_Plasmid, Phage_prediction, by="ContigID", all = TRUE)
AMR_MGE <- AMR_MGE %>% mutate_if(is.factor, fct_explicit_na, na_level = "-")
......
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