@@ -1,5 +1,5 @@

 Package: GSVA

-Version: 1.39.27

+Version: 1.39.28

 Title: Gene Set Variation Analysis for microarray and RNA-seq data

 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),

              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),

@@ -86,13 +86,10 @@ setMethod("gsva", signature(expr="SingleCellExperiment", gset.idx.list="list"),

   }

   expr <- assays(se)[[annotation]]

-  ## filter genes according to verious criteria,

+  ## filter genes according to various criteria,

   ## e.g., constant expression

-  if(is(expr, "dgCMatrix")){

-    expr <- .filterFeaturesSparse(expr, method)

-  } else {

-    expr <- .filterFeatures(expr, method)

-  }

+  

+  expr <- .filterFeatures(expr, method)

   ## map to the actual features for which expression data is available

   mapped.gset.idx.list <- .mapGeneSetsToFeatures(gset.idx.list, rownames(expr))

@@ -144,7 +141,7 @@ setMethod("gsva", signature(expr="dgCMatrix", gset.idx.list="list"),

   ## filter genes according to verious criteria,

   ## e.g., constant expression

-  expr <- .filterFeaturesSparse(expr, method)

+  expr <- .filterFeatures(expr, method)

   ## map to the actual features for which expression data is available

   mapped.gset.idx.list <- .mapGeneSetsToFeatures(gset.idx.list, rownames(expr))

@@ -66,27 +66,3 @@

   m@x <- unlist(x, use.names=FALSE)

   m

 }

-

-## filter out genes which non-zero values have

-## constant expression values

-.filterFeaturesSparse <- function(expr, method) {

-  

-  sdGenes <- sapply(.sparseToList(expr, 1), sd)

-  

-  if (any(sdGenes == 0) || any(is.na(sdGenes))) {

-    warning(sum(sdGenes == 0 | is.na(sdGenes)),

-            " genes with constant expression values throuhgout the samples.")

-    if (method != "ssgsea") {

-      warning("Since argument method!=\"ssgsea\", genes with constant expression values are discarded.")

-      expr <- expr[sdGenes > 0 & !is.na(sdGenes), ]

-    }

-  }

-  

-  if (nrow(expr) < 2)

-    stop("Less than two genes in the input assay object\n")

-  

-  if(is.null(rownames(expr)))

-    stop("The input assay object doesn't have rownames\n")

-  

-  expr

-}