Browse code

removed filterFeatureSparse()

pablo-rodr-bio2 authored on 03/05/2021 12:24:35
Showing3 changed files

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@@ -1,5 +1,5 @@
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 Package: GSVA
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-Version: 1.39.27
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+Version: 1.39.28
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 Title: Gene Set Variation Analysis for microarray and RNA-seq data
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 Authors@R: c(person("Justin", "Guinney", role=c("aut", "cre"), email="justin.guinney@sagebase.org"),
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              person("Robert", "Castelo", role="aut", email="robert.castelo@upf.edu"),
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@@ -86,13 +86,10 @@ setMethod("gsva", signature(expr="SingleCellExperiment", gset.idx.list="list"),
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   }
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   expr <- assays(se)[[annotation]]
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-  ## filter genes according to verious criteria,
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+  ## filter genes according to various criteria,
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   ## e.g., constant expression
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-  if(is(expr, "dgCMatrix")){
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-    expr <- .filterFeaturesSparse(expr, method)
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-  } else {
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-    expr <- .filterFeatures(expr, method)
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-  }
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+  
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+  expr <- .filterFeatures(expr, method)
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   ## map to the actual features for which expression data is available
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   mapped.gset.idx.list <- .mapGeneSetsToFeatures(gset.idx.list, rownames(expr))
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@@ -144,7 +141,7 @@ setMethod("gsva", signature(expr="dgCMatrix", gset.idx.list="list"),
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   ## filter genes according to verious criteria,
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   ## e.g., constant expression
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-  expr <- .filterFeaturesSparse(expr, method)
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+  expr <- .filterFeatures(expr, method)
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   ## map to the actual features for which expression data is available
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   mapped.gset.idx.list <- .mapGeneSetsToFeatures(gset.idx.list, rownames(expr))
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@@ -66,27 +66,3 @@
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   m@x <- unlist(x, use.names=FALSE)
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   m
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 }
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-
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-## filter out genes which non-zero values have
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-## constant expression values
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-.filterFeaturesSparse <- function(expr, method) {
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-  
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-  sdGenes <- sapply(.sparseToList(expr, 1), sd)
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-  
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-  if (any(sdGenes == 0) || any(is.na(sdGenes))) {
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-    warning(sum(sdGenes == 0 | is.na(sdGenes)),
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-            " genes with constant expression values throuhgout the samples.")
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-    if (method != "ssgsea") {
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-      warning("Since argument method!=\"ssgsea\", genes with constant expression values are discarded.")
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-      expr <- expr[sdGenes > 0 & !is.na(sdGenes), ]
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-    }
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-  }
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-  
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-  if (nrow(expr) < 2)
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-    stop("Less than two genes in the input assay object\n")
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-  
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-  if(is.null(rownames(expr)))
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-    stop("The input assay object doesn't have rownames\n")
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-  
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-  expr
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-}