Merge pull request #17 from YuLab-SMU/master

merge
YuLab-SMU · Nov 20, 2022 · 7e5674a · 7e5674a
2 parents c02c6d9 + 5bf60f8
commit 7e5674a
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Showing 5 changed files with 28 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: DOSE
 Type: Package
 Title: Disease Ontology Semantic and Enrichment analysis
-Version: 3.23.3
+Version: 3.25.0.001
 Authors@R: c( person(given = "Guangchuang", family = "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre")),
  person(given = "Li-Gen", family = "Wang", email = "reeganwang020@gmail.com", role = "ctb"),
  person(given = "Vladislav", family = "Petyuk", email = "petyuk@gmail.com", role = "ctb"),

diff --git a/Makefile b/Makefile
@@ -1,7 +1,7 @@
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGSRC := $(shell basename `pwd`)
-BIOCVER := RELEASE_3_15
+BIOCVER := RELEASE_3_16
 
 all: rd check clean
 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# DOSE 3.25.0.001
+
++ test whether slot in `GSON` object is NULL (e.g., `GSON@keytype`) when assigning it to enrichment result (2022-11-07, Mon)
+
+# DOSE 3.24.0
+
++ Bioconductor RELEASE_3_16 (2022-11-02, Wed)
+
 # DOSE 3.23.3
 
 + replace `DO.db` to `HDO.db` (2022-10-7, Fri) 

diff --git a/R/enricher_internal.R b/R/enricher_internal.R
@@ -177,9 +177,15 @@ enricher_internal <- function(gene,
  readable = FALSE
  )
  if (inherits(USER_DATA, "GSON")) {
- x@keytype <- USER_DATA@keytype
- x@organism <- USER_DATA@species
- x@ontology <- gsub(".*;", "", USER_DATA@gsname)
+ if (!is.null(USER_DATA@keytype)) {
+ x@keytype <- USER_DATA@keytype
+ }
+ if (!is.null(USER_DATA@species)) {
+ x@organism <- USER_DATA@species
+ } 
+ if (!is.null(USER_DATA@gsname)) {
+ x@ontology <- gsub(".*;", "", USER_DATA@gsname)
+ }
  }
  return (x)
 }

diff --git a/R/gsea.R b/R/gsea.R
@@ -186,9 +186,15 @@ GSEA_internal <- function(geneList,
  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)
+ if (!is.null(USER_DATA@keytype)) {
+ res@keytype <- USER_DATA@keytype
+ }
+ if (!is.null(USER_DATA@species)) {
+ res@organism <- USER_DATA@species
+ } 
+ if (!is.null(USER_DATA@gsname)) {
+ res@setType <- gsub(".*;", "", USER_DATA@gsname)
+ }
  }
  return(res)
 }