change default order, #60

YuLab-SMU · Dec 9, 2021 · 751ca5f · 751ca5f
1 parent a89a61e
commit 751ca5f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DOSE
 Type: Package
 Title: Disease Ontology Semantic and Enrichment analysis
-Version: 3.21.1
+Version: 3.21.1.9001
 Authors@R: c( person(given = "Guangchuang", family = "Yu",        email = "[email protected]",   role = c("aut", "cre")),
               person(given = "Li-Gen",      family = "Wang",      email = "[email protected]",   role = "ctb"),
               person(given = "Vladislav",   family = "Petyuk",    email = "[email protected]",          role = "ctb"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# DOSE 3.21.1.9001
+
++ update the default order of GSEA result (2021-12-09, Thu)
+  - if p.adjust is identical, sorted by `abs(NES)`
+
+
 # DOSE 3.21.1
 
 + upate DisGeNET and NCG data (2021-11-14, Sun)

diff --git a/R/gsea.R b/R/gsea.R
@@ -86,7 +86,7 @@ GSEA_fgsea <- function(geneList,
     res <- res[!is.na(res$pvalue),]
     res <- res[ res$pvalue <= pvalueCutoff, ]
     res <- res[ res$p.adjust <= pvalueCutoff, ]
-    idx <- order(res$pvalue, decreasing = FALSE)
+    idx <- order(res$p.adjust, -abs(res$NES), decreasing = FALSE)
     res <- res[idx, ]
 
     if (nrow(res) == 0) {
@@ -311,7 +311,7 @@ GSEA_DOSE <- function(geneList,
     res <- res[!is.na(res$pvalue),]
     res <- res[ res$pvalue <= pvalueCutoff, ]
     res <- res[ res$p.adjust <= pvalueCutoff, ]
-    idx <- order(res$pvalue, decreasing = FALSE)
+    idx <- order(res$p.adjust, -abs(res$NES), decreasing = FALSE)
     res <- res[idx, ]
 
     if (nrow(res) == 0) {