fixes leadingEdge for positive pathways (#1)

ctlab · Sep 20, 2024 · 82f17c9 · 82f17c9
1 parent eecbf6b
commit 82f17c9
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Showing 2 changed files with 16 additions and 9 deletions.
diff --git a/R/fgsea.R b/R/fgsea.R
@@ -148,22 +148,15 @@ calcGseaStat <- function(stats,
         res <- c(res, list(tops=tops, bottoms=bottoms))
     }
     if (returnLeadingEdge) {
-        leadingEdge <- if (maxP > -minP) {
-            S[seq_along(S) <= which.max(bottoms)]
-        } else if (maxP < -minP) {
-            rev(S[seq_along(S) >= which.min(bottoms)])
-        } else {
-            NULL
-        }
         switch(scoreType,
                std = leadingEdge <- if (maxP > -minP) {
-                   S[seq_along(S) <= which.max(bottoms)]
+                   S[seq_along(S) <= which.max(tops)]
                } else if (maxP < -minP) {
                    rev(S[seq_along(S) >= which.min(bottoms)])
                } else {
                    NULL
                },
-               pos = leadingEdge <- S[seq_along(S) <= which.max(bottoms)],
+               pos = leadingEdge <- S[seq_along(S) <= which.max(tops)],
                neg = leadingEdge <- rev(S[seq_along(S) >= which.min(bottoms)]))
 
         res <- c(res, list(leadingEdge=leadingEdge))

diff --git a/tests/testthat/test_gsea_stat.R b/tests/testthat/test_gsea_stat.R
@@ -40,6 +40,20 @@ test_that("calcGseaStats(returnLeadingEdge=TRUE) works", {
     expect_false(10 %in% gseaRes$leadingEdge)
 })
 
+test_that("leading edge is consistent", {
+    stats <- exampleRanks
+    pathway <- examplePathways[[1]]
+
+    set.seed(1)
+    gseaRes <- fgseaSimple(list(p=pathway), stats, nperm=2)
+    gseaResRev <- fgseaSimple(list(p=pathway), -stats, nperm=2)
+
+    expect_identical(gseaRes$leadingEdge, gseaResRev$leadingEdge)
+
+    gseaResPos <- fgseaSimple(list(p=pathway), stats, nperm=2, scoreType = "pos")
+    expect_identical(gseaRes$leadingEdge, gseaResPos$leadingEdge)
+})
+
 test_that("calcGseaStats returns zero when both sides are equally enriched", {
     stats <- 10:-10
     sample <- 10:12