--- a/GO-enrich.R	Tue Nov 06 08:56:05 2018 -0500
+++ b/GO-enrich.R	Wed Nov 21 08:22:13 2018 -0500
@@ -264,12 +264,14 @@
   for (onto in ontology) {
     if (args$go_represent == "true") {
       ggo<-repartition.GO(gene, orgdb, onto, level, readable=TRUE)
+      ggo <- as.data.frame(apply(ggo, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" and " " to NA
       output_path = paste("cluster_profiler_GGO_",onto,".tsv",sep="")
       write.table(ggo, output_path, sep="\t", row.names = FALSE, quote = FALSE )
     }
 
     if (args$go_enrich == "true") {
       ego<-enrich.GO(gene, universe_gene, orgdb, onto, pval_cutoff, qval_cutoff,plot)
+      ego <- as.data.frame(apply(ego, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" and " " to NA
       output_path = paste("cluster_profiler_EGO_",onto,".tsv",sep="")
       write.table(ego, output_path, sep="\t", row.names = FALSE, quote = FALSE )
     }