annotate arg id 'NULL' update

DESCRIPTION

 Package: ViSEAGO
-Version: 0.99.35
+Version: 0.99.36
 Title: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
 Author: Aurelien Brionne [aut, cre],
         Amelie Juanchich [aut],

NEWS

@@ -18,3 +18,7 @@ CHANGES IN VERSION 0.99.34
 CHANGES IN VERSION 0.99.35
 ------------------------
  o README update
+
+CHANGES IN VERSION 0.99.36
+------------------------
+ o annotate id argument signature with "NULL"

R/annotate.R

@@ -107,7 +107,7 @@
 #' # display organisms supported by NCBI EntrezGene orthologs pipeline
 #' EntrezGene<-ViSEAGO::EntrezGene2GO()
 #' ViSEAGO::annotate(
-#'     id=NULL,
+#'     id="NULL",
 #'     object=EntrezGene,
 #'     ortholog=TRUE
 #' )
@@ -165,7 +165,7 @@ setMethod(
             )
 
             # select the target species and ortholog
-            if(is.null(id)){
+            if(id=="NULL"){
 
                 # ordering by Scientific name
                 setorderv(

README.md

@@ -27,7 +27,7 @@ remotes::install_gitlab(
     devtools::build("ViSEAGO")
 
     # install package (from R console)
-    install.packages("ViSEAGO_0.99.34.tar.gz", repos = NULL, type = "source")
+    install.packages("ViSEAGO_0.99.36.tar.gz", repos = NULL, type = "source")
 ```
 
 ## Citation

man/annotate-methods.Rd

@@ -108,7 +108,7 @@ myGENE2GO<-ViSEAGO::annotate(
 # display organisms supported by NCBI EntrezGene orthologs pipeline
 EntrezGene<-ViSEAGO::EntrezGene2GO()
 ViSEAGO::annotate(
-    id=NULL,
+    id="NULL",
     object=EntrezGene,
     ortholog=TRUE
 )

man/merge_enrich_terms-methods.Rd

@@ -45,30 +45,30 @@ background_L<-scan(
 
 ###################
 # load Differentialy Expressed (DE) gene identifiants from files
-L_pregnantvslactateDE<-scan(
+PregnantvslactateDE<-scan(
     system.file(
         "extdata/data/input",
-        "L_pregnantvslactateDE.txt",
+        "pregnantvslactateDE.txt",
         package = "ViSEAGO"
     ),
     quiet=TRUE,
     what=""
 )
 
-L_virginvslactateDE<-scan(
+VirginvslactateDE<-scan(
     system.file(
         "extdata/data/input",
-        "L_virginvslactateDE.txt",
+        "virginvslactateDE.txt",
         package = "ViSEAGO"
     ),
     quiet=TRUE,
     what=""
 )
 
-L_virginvspregnantDE<-scan(
+VirginvspregnantDE<-scan(
     system.file(
         "extdata/data/input",
-        "L_virginvspregnantDE.txt",
+        "virginvspregnantDE.txt",
         package="ViSEAGO"
     ),
     quiet=TRUE,
@@ -77,24 +77,24 @@ L_virginvspregnantDE<-scan(
 \dontrun{
 ###################
 # create topGOdata for BP for each list of DE genes
-BP_L_pregnantvslactate<-ViSEAGO::create_topGOdata(
-    geneSel=L_pregnantvslactateDE,
+BP_Pregnantvslactate<-ViSEAGO::create_topGOdata(
+    geneSel=PregnantvslactateDE,
     allGenes=background_L,
     gene2GO=myGENE2GO,
     ont="BP",
     nodeSize=5
 )
 
-BP_L_virginvslactate<-ViSEAGO::create_topGOdata(
-    geneSel=L_virginvslactateDE,
+BP_Virginvslactate<-ViSEAGO::create_topGOdata(
+    geneSel=VirginvslactateDE,
     allGenes=background_L,
     gene2GO=myGENE2GO,
     ont="BP",
     nodeSize=5
 )
 
-BP_L_virginvspregnant<-ViSEAGO::create_topGOdata(
-    geneSel=L_virginvspregnantDE,
+BP_Virginvspregnant<-ViSEAGO::create_topGOdata(
+    geneSel=VirginvspregnantDE,
     allGenes=background_L,
     gene2GO=myGENE2GO,
     ont="BP",
@@ -103,19 +103,19 @@ BP_L_virginvspregnant<-ViSEAGO::create_topGOdata(
 
 ###################
 # perform TopGO tests
-elim_BP_L_pregnantvslactate<-topGO::runTest(
+elim_BP_Pregnantvslactate<-topGO::runTest(
     BP_L_pregnantvslactate,
     algorithm ="elim",
     statistic = "fisher"
 )
 
-elim_BP_L_virginvslactate<-topGO::runTest(
+elim_BP_Virginvslactate<-topGO::runTest(
     BP_L_virginvslactate,
     algorithm ="elim",
     statistic = "fisher"
 )
 
-elim_BP_L_virginvspregnant<-topGO::runTest(
+elim_BP_Virginvspregnant<-topGO::runTest(
     BP_L_virginvspregnant,
     algorithm ="elim",
     statistic = "fisher"
@@ -125,9 +125,9 @@ elim_BP_L_virginvspregnant<-topGO::runTest(
 # merge topGO results
 BP_sResults<-ViSEAGO::merge_enrich_terms(
     Input=list(
-        L_pregnantvslactate=c("BP_L_pregnantvslactate","elim_BP_L_pregnantvslactate"),
-        L_virginvslactate=c("BP_L_virginvslactate","elim_BP_L_virginvslactate"),
-        L_virginvspregnant=c("BP_L_virginvspregnant","elim_BP_L_virginvspregnant")
+        Pregnantvslactate=c("BP_Pregnantvslactate","elim_BP_Pregnantvslactate"),
+        Virginvslactate=c("BP_Virginvslactate","elim_BP_Virginvslactate"),
+        Virginvspregnant=c("BP_Virginvspregnant","elim_BP_Virginvspregnant")
     )
 )
 }