Improvement v2 to taxonomy parsing

jbisanz · Oct 19, 2018 · 195b4c0 · 195b4c0
1 parent 337067a
commit 195b4c0
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/R/qza_to_phyloseq.R b/R/qza_to_phyloseq.R
@@ -37,7 +37,7 @@ qza_to_phyloseq<-function(features,tree,taxonomy,metadata, tmp){
     taxt<-strsplit(as.character(taxonomy$Taxon),"\\; ")
     taxt<-lapply(taxt, function(x){length(x)=7;return(x)})
     taxt<-do.call(rbind, taxt)
-    taxt<-apply(taxt,2, function(x) replace(x, grepl("^[kpcofgs]__$", x), "Not_Assigned"))
+    taxt<-apply(taxt,2, function(x) replace(x, grepl("^[kpcofgs]__$", x), NA))
     rownames(taxt)<-taxonomy$Feature.ID
     colnames(taxt)<-c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
     argstring<-paste(argstring, "tax_table(taxt),")