update

huerqiang · Jun 8, 2022 · 838c767 · 838c767
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Showing 3 changed files with 14 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DOSE
 Type: Package
 Title: Disease Ontology Semantic and Enrichment analysis
-Version: 3.23.1
+Version: 3.23.2
 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 +1,7 @@
+# DOSE 3.23.2
+
++ Support `GSON` object in `GSEA_internal()` (2022-06-08, Wed)
+
 # DOSE 3.23.1
 
 + Support `GSON` object in `enricher_internal()` (2022-06-06, Mon)

diff --git a/R/utilities.R b/R/utilities.R
@@ -400,7 +400,15 @@ is.sorted <- function(x, decreasing=TRUE) {
 }
 
 getGeneSet <- function(USER_DATA) {
-    get("PATHID2EXTID", envir = USER_DATA)
+    if (inherits(USER_DATA, "environment")) { 
+        res <- get("PATHID2EXTID", envir = USER_DATA)
+    } else if (inherits(USER_DATA, "GSON")) {
+        gsid2gene <- USER_DATA@gsid2gene
+        res <- split(gsid2gene$gene, gsid2gene$gsid) 
+    } else {
+        stop("not supported")
+    }
+    return(res)
 }