Merge pull request #1397 from bigomics/fix-3172-gsettable

fix gene-in-gsets table (sub-issue 1372)

Author: ivokwee

components/board.expression/R/expression_server.R

@@ -573,10 +573,13 @@ ExpressionBoard <- function(id, pgx, labeltype = shiny::reactive("feature")) {
       if (is.null(sel.row)) {
         return(NULL)
       }
-      gene1 <- res[sel.row, ]
-
-      gmt_gene_mapping <- ifelse(is.na(gene1$human_ortholog), gene1$symbol, gene1$human_ortholog)
 
+      ## determine which column to match with pgx$GMT
+      gene1 <- res[sel.row, ]
+      match.res <- apply(res[,c("symbol","human_ortholog")],2,
+        function(x) sum(x%in%rownames(pgx$GMT)))
+      match.col <- names(which.max(match.res))
+      gmt_gene_mapping <- gene1[,match.col]
       j <- which(rownames(pgx$GMT) == gmt_gene_mapping)
       if (length(j) == 0) {
         return(NULL)