add missing import

Author: mass-a

NAMESPACE

@@ -27,4 +27,5 @@ importFrom(stats,cutree)
 importFrom(stats,dist)
 importFrom(stats,hclust)
 importFrom(utils,head)
+importFrom(utils,packageVersion)
 importFrom(viridis,viridis)

R/main.R

@@ -36,6 +36,7 @@
 #' geneNMF_programs <- multiNMF(list(sampleObj), k=5)
 #' 
 #' @importFrom RcppML nmf
+#' @importFrom utils packageVersion
 #' @export  
 multiNMF <- function(obj.list, assay="RNA", slot="data", k=5:6,
                    hvg=NULL, nfeatures = 2000, L1=c(0,0),
@@ -573,6 +574,7 @@ runGSEA <- function(genes, universe=NULL,
 #' sampleObj <- runNMF(sampleObj, k=8)
 #' @importFrom RcppML nmf
 #' @importFrom methods new
+#' @importFrom utils packageVersion
 #' @export  
 runNMF <- function(obj, assay="RNA", slot="data", k=10,
                    new.reduction="NMF", seed=123,

R/utils.R

@@ -90,7 +90,7 @@ get_metaprogram_consensus <- function(nmf.wgt,
 
   markers.consensus <- lapply(seq(1, nMP), function(c) {
     which.samples <- names(cl_members)[cl_members == c]
-    gene.table <- GeneNMF:::geneList2table(nmf.wgt)[,which.samples]
+    gene.table <- geneList2table(nmf.wgt)[,which.samples]
 
     genes.avg <- apply(as.matrix(gene.table), 1, function(x){
       mean <- mean(x)