Updated AMR_MGE.R

rules/AMR/AMR_MGE.R

@@ -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 = "-")