data

noriakis · Mar 28, 2024 · 92ab840 · 92ab840
1 parent 5ea0265
commit 92ab840
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Showing 4 changed files with 9 additions and 2 deletions.
diff --git 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
@@ -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
diff --git a/man/consensusSeqGeneral.Rd b/man/consensusSeqGeneral.Rd