fix tax table conversion to taxonomyTable by coercing manually data frame to matrix

R/generate_phyloseq_fun.R

@@ -52,7 +52,8 @@ generate_phyloseq_fun <- function(dada_res = dada_res, tax.table = tax.table, tr
   names(sequences) <- sapply(sequences,digest,algo='md5')
 
   if(class(tax.table) == "data.frame"){
-	  TAX=tax_table(tax.table)
+	  # need to coerce manually data frame to matrix before converting to taxonomyTable
+	  TAX=tax_table(as.matrix(tax.table))
   } else {
 	  stop(paste0("Unexpected class for tax.table object: ", class(tax.table), ". Should be a data frame."))
   }