check for empty strings in gene names, fixes #149

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fgsea
 Title: Fast Gene Set Enrichment Analysis
-Version: 1.31.2
+Version: 1.31.3
 Authors@R: c(person("Gennady", "Korotkevich", role = "aut"),
              person("Vladimir", "Sukhov", role = "aut"),
              person("Nikolay", "Budin", role = "ctb"),

NEWS

@@ -1,3 +1,6 @@
+CHANGES IN VERSION 1.31.3
+* check for empty strings in gene names
+
 CHANGES IN VERSION 1.31.2
 * fora() provides fold enrichment scores for more effective prioritisation of results
 

R/fgsea.R

@@ -39,26 +39,6 @@ fgsea <- function(pathways, stats, minSize = 1, maxSize = length(stats)-1, gseaP
 
 
 preparePathwaysAndStats <- function(pathways, stats, minSize, maxSize, gseaParam, scoreType){
-    # Error if pathways is not a list
-    if (!is.list(pathways)) {
-        stop("pathways should be a list with each element containing names of the stats argument")
-    }
-
-    # Error if stats is not named
-    if (is.null(names(stats))) {
-        stop("stats should be named")
-    }
-
-    # Error if stats names are NA
-    if (any(is.na(names(stats)))) {
-        stop("NAs in names(stats) are not allowed")
-    }
-
-    # Error for duplicate gene names
-    if (any(duplicated(names(stats)))) {
-        stop("Duplicate names(stats) are not allowed")
-    }
-
     # Error if stats are non-finite
     if (any(!is.finite(stats))){
         stop("Not all stats values are finite numbers")
@@ -81,21 +61,11 @@ preparePathwaysAndStats <- function(pathways, stats, minSize, maxSize, gseaParam
     stats <- sort(stats, decreasing=TRUE)
     stats <- abs(stats) ^ gseaParam
 
+    res <- preparePathways(pathways, universe=names(stats), minSize, maxSize)
 
-    minSize <- max(minSize, 1)
-    maxSize <- min(maxSize, length(stats)-1)
+    res$stats <- stats
 
-    pathwaysFiltered <- lapply(pathways, function(p) { unique(na.omit(fmatch(p, names(stats)))) })
-    pathwaysSizes <- sapply(pathwaysFiltered, length)
-
-    toKeep <- which(minSize <= pathwaysSizes & pathwaysSizes <= maxSize)
-
-    pathwaysFiltered <- pathwaysFiltered[toKeep]
-    pathwaysSizes <- pathwaysSizes[toKeep]
-
-    list(filtered=pathwaysFiltered,
-         sizes=pathwaysSizes,
-         stats=stats)
+    res
 }
 
 

R/fgseaORA.R

@@ -22,25 +22,12 @@
 #' data(exampleRanks)
 #' foraRes <- fora(examplePathways, genes=tail(names(exampleRanks), 200), universe=names(exampleRanks))
 fora <- function(pathways, genes, universe, minSize=1, maxSize=length(universe)-1) {
-    # Error if pathways is not a list
-    if (!is.list(pathways)) {
-        stop("pathways should be a list with each element containing genes from the universe")
-    }
-
-    # Warning message for duplicate gene names
-    if (any(duplicated(universe))) {
-        warning("There were duplicate genes in universe, they were collapsed")
-        universe <- unique(universe)
-    }
-
-    minSize <- max(minSize, 1)
+    pp <- preparePathways(pathways, universe, minSize, maxSize)
+    pathwaysFiltered <- pp$filtered
+    pathwaysSizes <- pp$sizes
 
-    pathwaysFiltered <- lapply(pathways, function(p) { unique(na.omit(fmatch(p, universe))) })
-    pathwaysSizes <- sapply(pathwaysFiltered, length)
 
-    toKeep <- which(minSize <= pathwaysSizes & pathwaysSizes <= maxSize)
-
-    if (length(toKeep) == 0){
+    if (length(pathwaysFiltered) == 0){
         return(data.table(pathway=character(),
                           pval=numeric(),
                           padj=numeric(),
@@ -50,13 +37,11 @@ fora <- function(pathways, genes, universe, minSize=1, maxSize=length(universe)-
                           overlapGenes=list()))
     }
 
-    pathwaysFiltered <- pathwaysFiltered[toKeep]
-    pathwaysSizes <- pathwaysSizes[toKeep]
-
 
     if (!all(genes %in% universe)) {
         warning("Not all of the input genes belong to the universe, such genes were removed")
     }
+
     genesFiltered <- unique(na.omit(fmatch(genes, universe)))
 
     overlaps <- lapply(pathwaysFiltered, intersect, genesFiltered)

R/geseca-utils.R

@@ -26,18 +26,9 @@ checkGesecaArgs <- function(E, pathways){
 }
 
 gesecaPreparePathways <- function(E, pathways, minSize, maxSize){
-    minSize <- max(minSize, 1)
-    maxSize <- min(nrow(E) - 1, maxSize)
+    res <- preparePathways(pathways, universe = rownames(E), minSize, maxSize)
 
-    pathwaysFiltered <- lapply(pathways, function(p) {unique(na.omit(fmatch(p, rownames(E))))})
-    pathwaysSizes <- sapply(pathwaysFiltered, length)
-
-    toKeep <- which(minSize <= pathwaysSizes & pathwaysSizes <= maxSize)
-    pathwaysFiltered <- pathwaysFiltered[toKeep]
-    pathwaysSizes <- pathwaysSizes[toKeep]
-
-    return(list(filtered=pathwaysFiltered,
-                sizes=pathwaysSizes))
+    return(res)
 }
 
 

R/util.R

@@ -0,0 +1,45 @@
+preparePathways <- function(pathways, universe, minSize, maxSize){
+    universeArg <- deparse(match.call()$universe)
+    # Error if pathways is not a list
+    if (!is.list(pathways)) {
+        stop("pathways should be a list with each element containing gene identifiers")
+    }
+
+    # Error if stats is not named
+    if (is.null(universe)) {
+        .stopf("%s should not be null", universeArg)
+    }
+
+    # Error if stats names are NA
+    if (any(is.na(universe))) {
+        .stopf("NAs in %s are not allowed", universeArg)
+    }
+
+    # Error if stats names are empty string
+    if (any(universe == "")) {
+        .stopf("Empty strings are not allowed in %s", universeArg)
+    }
+
+    # Error for duplicate gene names
+    if (any(duplicated(universe))) {
+        .stopf("Duplicate values in %s not allowed", universeArg)
+    }
+
+    minSize <- max(minSize, 1)
+    maxSize <- min(maxSize, length(universe)-1)
+
+    pathwaysFiltered <- lapply(pathways, function(p) { unique(na.omit(fmatch(p, universe))) })
+    pathwaysSizes <- lengths(pathwaysFiltered)
+
+    toKeep <- which(minSize <= pathwaysSizes & pathwaysSizes <= maxSize)
+
+    pathwaysFiltered <- pathwaysFiltered[toKeep]
+    pathwaysSizes <- pathwaysSizes[toKeep]
+
+    list(filtered=pathwaysFiltered,
+         sizes=pathwaysSizes)
+}
+
+.stopf <- function(fmt, ...) {
+    stop(sprintf(fmt, ...))
+}

tests/testthat/test_gsea_analysis.R

@@ -126,6 +126,10 @@ test_that("fgseaSimple correctly checks gene names", {
     names(ranks)[41] <- NA
     expect_error(fgseaSimple(examplePathways, ranks, nperm=100, minSize=10, maxSize=50, nproc=1))
 
+    ranks <- exampleRanks
+    names(ranks)[41] <- ""
+    expect_error(fgseaSimple(examplePathways, ranks, nperm=100, minSize=10, maxSize=50, nproc=1))
+
     ranks <- unname(exampleRanks)
     expect_error(fgseaSimple(examplePathways, ranks, nperm=100, minSize=10, maxSize=50, nproc=1))