diff --git a/R/NMF.R b/R/NMF.R
index 6a9fcba..19eb658 100644
--- a/R/NMF.R
+++ b/R/NMF.R
@@ -157,7 +157,11 @@ NMF <- function(stana, species, rank=3, target="KO", seed=53, method="snmf/r",
 
     cat("Present feature per factor:", apply(basisMat!=0, 2, function(x) sum(x)), "\n")
     stana@NMF[[species]] <- res
-    return(stana)
+    if (estimate & !nnlm_flag) {
+        return(list(stana, test))
+    } else {
+        return(stana)    
+    }
 }
 
 #' plotStackedBarPlot
diff --git a/R/utils.R b/R/utils.R
index d758443..6e64a67 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -69,7 +69,7 @@ listToNV <- function(l) {
 #' @export
 #' @return ggplot
 plotSNVInfo <- function(stana, sp) {
-	if (!is.null(stana@includeSNVID)[[sp]]) {cat_subtle("# The set SNV ID information is not used in this function\n")}
+	if (!is.null(stana@includeSNVID[[sp]])) {cat_subtle("# The set SNV ID information is not used in this function\n")}
     d <- stana@snpsInfo[[sp]]
     tbl <- data.frame(table(paste0(d$major_allele,"/",d$minor_allele)))
     if ("locus_type" %in% colnames(d)) {
diff --git a/inst/extdata/sysdata.rda b/inst/extdata/sysdata.rda
index a709907..fd63734 100644
Binary files a/inst/extdata/sysdata.rda and b/inst/extdata/sysdata.rda differ
diff --git a/man/consensusSeqGeneral.Rd b/man/consensusSeqGeneral.Rd
index 2b74a0c..bcfe64d 100644
--- a/man/consensusSeqGeneral.Rd
+++ b/man/consensusSeqGeneral.Rd
@@ -12,6 +12,7 @@ consensusSeqGeneral(
   output_seq = FALSE,
   tree = FALSE,
   return_mat = FALSE,
+  allele_columns = c("major_allele", "minor_allele"),
   verbose = FALSE
 )
 }
@@ -30,6 +31,8 @@ consensusSeqGeneral(
 
 \item{return_mat}{return matrix of characters}
 
+\item{allele_columns}{columns specifying major and minor allele}
+
 \item{verbose}{output current status}
 }
 \description{