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

 Package: GSVA

-Version: 1.39.11

+Version: 1.39.12

 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"),

@@ -26,19 +26,8 @@ setMethod("gsva", signature(expr="HDF5Array", gset.idx.list="list"),

   ## e.g., constant expression

   expr <- .filterFeatures(expr, method)

-  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")

-  

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

-  mapped.gset.idx.list <- lapply(gset.idx.list,

-                                 function(x, y) na.omit(fastmatch::fmatch(x, y)),

-                                 rownames(expr))

-  

-  if (length(unlist(mapped.gset.idx.list, use.names=FALSE)) == 0)

-    stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")

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

   ## remove gene sets from the analysis for which no features are available

   ## and meet the minimum and maximum gene-set size specified by the user

@@ -105,20 +94,8 @@ setMethod("gsva", signature(expr="SingleCellExperiment", gset.idx.list="list"),

     expr <- .filterFeatures(expr, method)

   }

-  

-  if (nrow(expr) < 2)

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

-  

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

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

-  

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

-  mapped.gset.idx.list <- lapply(gset.idx.list,

-                                 function(x, y) na.omit(fastmatch::fmatch(x, y)),

-                                 rownames(expr))

-  

-  if (length(unlist(mapped.gset.idx.list, use.names=FALSE)) == 0)

-    stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")

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

   ## remove gene sets from the analysis for which no features are available

   ## and meet the minimum and maximum gene-set size specified by the user

@@ -169,19 +146,8 @@ setMethod("gsva", signature(expr="dgCMatrix", gset.idx.list="list"),

   ## e.g., constant expression

   expr <- .filterFeaturesSparse(expr, method)

-  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")

-  

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

-  mapped.gset.idx.list <- lapply(gset.idx.list,

-                                 function(x, y) na.omit(fastmatch::fmatch(x, y)),

-                                 rownames(expr))

-  

-  if (length(unlist(mapped.gset.idx.list, use.names=FALSE)) == 0)

-    stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")

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

   ## remove gene sets from the analysis for which no features are available

   ## and meet the minimum and maximum gene-set size specified by the user

@@ -243,12 +209,6 @@ setMethod("gsva", signature(expr="SummarizedExperiment", gset.idx.list="GeneSetC

   ## e.g., constant expression

   expr <- .filterFeatures(expr, method)

-  if (nrow(expr) < 2)

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

-  

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

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

-

   annotpkg <- metadata(se)$annotation

   if (!is.null(annotpkg) && length(annotpkg) > 0 && is.character(annotpkg) && annotpkg != "") {

     if (!annotpkg %in% installed.packages())

@@ -272,12 +232,7 @@ setMethod("gsva", signature(expr="SummarizedExperiment", gset.idx.list="GeneSetC

   }

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

-  mapped.gset.idx.list <- lapply(mapped.gset.idx.list,

-                                 function(x, y) na.omit(fastmatch::fmatch(x, y)),

-                                 rownames(expr))

-

-  if (length(unlist(mapped.gset.idx.list, use.names=FALSE)) == 0)

-    stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")

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

   ## remove gene sets from the analysis for which no features are available

   ## and meet the minimum and maximum gene-set size specified by the user

@@ -344,20 +299,9 @@ setMethod("gsva", signature(expr="SummarizedExperiment", gset.idx.list="list"),

   ## e.g., constant expression

   expr <- .filterFeatures(expr, method)

-  if (nrow(expr) < 2)

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

-  

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

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

-

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

-  mapped.gset.idx.list <- lapply(gset.idx.list,

-                                 function(x, y) na.omit(fastmatch::fmatch(x, y)),

-                                 rownames(expr))

-

-  if (length(unlist(mapped.gset.idx.list, use.names=FALSE)) == 0)

-    stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")

-

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

+  

   ## remove gene sets from the analysis for which no features are available

   ## and meet the minimum and maximum gene-set size specified by the user

   mapped.gset.idx.list <- filterGeneSets(mapped.gset.idx.list,

@@ -409,20 +353,9 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="list"),

   ## e.g., constant expression

   expr <- .filterFeatures(expr, method)

-  if (nrow(expr) < 2)

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

-  

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

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

-

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

-  mapped.gset.idx.list <- lapply(gset.idx.list,

-                                 function(x, y) na.omit(fastmatch::fmatch(x, y)),

-                                 rownames(expr))

-

-  if (length(unlist(mapped.gset.idx.list, use.names=FALSE)) == 0)

-    stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")

-

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

+  

   ## remove gene sets from the analysis for which no features are available

   ## and meet the minimum and maximum gene-set size specified by the user

   mapped.gset.idx.list <- filterGeneSets(mapped.gset.idx.list,

@@ -472,12 +405,6 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="GeneSetCollecti

   ## e.g., constant expression

   expr <- .filterFeatures(expr, method)

-  if (nrow(expr) < 2)

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

-  

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

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

-

   annotpkg <- Biobase::annotation(eset)

   if (length(annotpkg) > 0 && annotpkg != "") {

     if (!annotpkg %in% installed.packages())

@@ -501,14 +428,11 @@ setMethod("gsva", signature(expr="ExpressionSet", gset.idx.list="GeneSetCollecti

   }

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

-  tmp <- lapply(mapped.gset.idx.list,

-                function(x, y) na.omit(fastmatch::fmatch(x, y)),

-                rownames(expr))

-  names(tmp) <- names(mapped.gset.idx.list)

-

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

+  

   ## remove gene sets from the analysis for which no features are available

   ## and meet the minimum and maximum gene-set size specified by the user

-  mapped.gset.idx.list <- filterGeneSets(tmp,

+  mapped.gset.idx.list <- filterGeneSets(mapped.gset.idx.list,

                                          min.sz=max(1, min.sz),

                                          max.sz=max.sz)

@@ -553,12 +477,6 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="GeneSetCollection"),

   ## e.g., constant expression

   expr <- .filterFeatures(expr, method)

-  if (nrow(expr) < 2)

-    stop("Less than two genes in the input expression data matrix\n")

-  

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

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

-

   ## map gene identifiers of the gene sets to the features in the matrix

   mapped.gset.idx.list <- gset.idx.list

   if (!missing(annotation)) {

@@ -570,17 +488,11 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="GeneSetCollection"),

   }

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

-  tmp <- lapply(geneIds(mapped.gset.idx.list),

-                                 function(x, y) na.omit(fastmatch::fmatch(x, y)),

-                                 rownames(expr))

-  names(tmp) <- names(mapped.gset.idx.list)

-

-  if (length(unlist(tmp, use.names=FALSE)) == 0)

-    stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")

-

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

+  

   ## remove gene sets from the analysis for which no features are available

   ## and meet the minimum and maximum gene-set size specified by the user

-  mapped.gset.idx.list <- filterGeneSets(tmp,

+  mapped.gset.idx.list <- filterGeneSets(mapped.gset.idx.list,

                                          min.sz=max(1, min.sz),

                                          max.sz=max.sz)

@@ -623,16 +535,9 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="list"),

   ## e.g., constant expression

   expr <- .filterFeatures(expr, method)

-  if (nrow(expr) < 2)

-    stop("Less than two genes in the input expression data matrix\n")

-

-  mapped.gset.idx.list <- lapply(gset.idx.list,

-                                 function(x ,y) na.omit(fastmatch::fmatch(x, y)),

-                                 rownames(expr))

-

-  if (length(unlist(mapped.gset.idx.list, use.names=FALSE)) == 0)

-    stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")

-

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

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

+  

   ## remove gene sets from the analysis for which no features are available

   ## and meet the minimum and maximum gene-set size specified by the user

   mapped.gset.idx.list <- filterGeneSets(mapped.gset.idx.list,

@@ -1091,10 +996,10 @@ setMethod("computeGeneSetsOverlap", signature(gSets="list", uniqGenes="character

           function(gSets, uniqGenes, min.sz=1, max.sz=Inf) {

   totalGenes <- length(uniqGenes)

-  ## map to the features requested

-  gSets <- lapply(gSets, function(x, y) as.vector(na.omit(fastmatch::fmatch(x, y))), uniqGenes)

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

+  gSets <- .mapGeneSetsToFeatures(gSets, uniqGenes)

-  lenGsets <- sapply(gSets, length)

+  lenGsets <- lengths(gSets)

   totalGsets <- length(gSets)

   gSetsMembershipMatrix <- matrix(0, nrow=totalGenes, ncol=totalGsets,

@@ -1111,9 +1016,9 @@ setMethod("computeGeneSetsOverlap", signature(gSets="list", uniqGenes="Expressio

   totalGenes <- length(uniqGenes)

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

-  gSets <- lapply(gSets, function(x, y) as.vector(na.omit(fastmatch::fmatch(x, y))), uniqGenes)

+  gSets <- .mapGeneSetsToFeatures(gSets, uniqGenes)

-  lenGsets <- sapply(gSets, length)

+  lenGsets <- lengths(gSets)

   totalGsets <- length(gSets)

   gSetsMembershipMatrix <- matrix(0, nrow=totalGenes, ncol=totalGsets,

@@ -13,9 +13,41 @@

     }

   } 

+  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

 }

+## maps gene sets content in 'gsets' to 'features', where 'gsets'

+## is a 'list' object with character string vectors as elements,

+## and 'features' is a character string vector object. it assumes

+## features in both input objects follow the same nomenclature,

+.mapGeneSetsToFeatures <- function(gsets, features) {

+

+  ## fastmatch::fmatch() modifies the 'table' argument (i.e., the

+  ## second argument) in place by adding the attribute '.match.hash'

+  ## https://github.com/rcastelo/GSVA/issues/39

+  ## to avoid that undesired feature we duplicate 'features'

+  ## by adding an "impossible value" at the end and let

+  ## fastmatch::match() work with the duplicated object

+  features2 <- c(features, "&!%impossiblevalue%!&")

+

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

+  mapdgenesets <- lapply(gsets,

+                         function(x, y)

+                           as.vector(na.omit(fastmatch::fmatch(x, y))),

+                         features2)

+  

+  if (length(unlist(mapdgenesets, use.names=FALSE)) == 0)

+    stop("No identifiers in the gene sets could be matched to the identifiers in the expression data.")

+

+  mapdgenesets

+}

+

 ## transforms a dgCMatrix into a list of its

 ## non-zero values by MARGIN (1 for row, 2 for column)

 .sparseToList <-function(dgCMat, MARGIN){

@@ -58,5 +90,11 @@

     }

   }

+  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

-}

\ No newline at end of file

+}