add values of organism, keytype and ontology for `enricher_inte…

…rnal()`

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DOSE
 Type: Package
 Title: Disease Ontology Semantic and Enrichment analysis
-Version: 3.23.2.001
+Version: 3.23.2.002
 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"),
@@ -46,4 +46,4 @@ BugReports: https://github.com/GuangchuangYu/DOSE/issues
 Packaged: 2011-12-28 08:16:14 UTC; root
 biocViews: Annotation, Visualization, MultipleComparison, GeneSetEnrichment,
     Pathways, Software
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1

NEWS.md

@@ -1,5 +1,6 @@
-# DOSE 3.23.2.001
+# DOSE 3.23.2.002
 
++ add values of  `organism`, `keytype` and `ontology` for `enricher_internal()` (2022-09-21, Wed)
 + move `inst/extdata/parse-obo.R` to `HDO.db` package (2022-08-29, Mon) 
 + rename `qvalues` to `qvalue` in `gseaResult` object (2022-08-29, Mon)
 

R/enricher_internal.R

@@ -176,6 +176,11 @@ enricher_internal <- function(gene,
              ontology       = "UNKNOWN",
              readable       = FALSE
              )
+    if (inherits(USER_DATA, "GSON")) {
+        x@keytype <- USER_DATA@keytype
+        x@organism <- USER_DATA@species
+        x@ontology <- gsub(".*;", "", USER_DATA@gsname)
+    }
     return (x)
 }
 

R/gsea.R

@@ -185,6 +185,11 @@ GSEA_internal <- function(geneList,
     res@organism <- "UNKNOWN"
     res@setType <- "UNKNOWN"
     res@keytype <- "UNKNOWN"
+    if (inherits(USER_DATA, "GSON")) {
+        res@keytype <- USER_DATA@keytype
+        res@organism <- USER_DATA@species
+        res@setType <- gsub(".*;", "", USER_DATA@gsname)
+    }
     return(res)
 }
 
@@ -351,6 +356,7 @@ GSEA_DOSE <- function(geneList,
         params     = params,
         readable   = FALSE
         )
+
 }