Ensemble 2GO()default biomart connector update

DESCRIPTION

 Package: ViSEAGO
-Version: 1.3.1
+Version: 1.3.2
 Title: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
 Author: Aurelien Brionne [aut, cre],
         Amelie Juanchich [aut],

NEWS

@@ -68,4 +68,5 @@ CHANGES IN VERSION 1.2
 CHANGES IN VERSION 1.3
 ------------------------
  o print graph with orca
+ o Ensembl2GO() biomart update
 

R/Ensembl2GO.R

@@ -2,7 +2,7 @@
 #' @description  List Ensembl referenced organisms datasets from the current (NULL) or archive (number in \code{character}) annotation version.
 #' @importFrom biomaRt useEnsembl listEnsembl listDatasets
 #' @importFrom data.table data.table
-#' @param biomart the biomart name (eg. "ensembl", the default) available with \pkg{biomaRt} package \code{\link[biomaRt]{listEnsembl}}.
+#' @param biomart the biomart name (eg. "genes", the default) available with \pkg{biomaRt} package \code{\link[biomaRt]{listEnsembl}}.
 #' @param host the Ensembl host adress for \href{http://www.ensembl.org/index.html}{vertebrate} ("www.ensembl.org", the default value),
 #' \href{http://www.plants.ensembl.org/index.html}{plants} ("plants.ensembl.org"),
 #' \href{http://www.metazoa.ensembl.org/index.html}{metazoa} ("metazoa.ensembl.org"),
@@ -35,17 +35,17 @@
 #' \dontrun{
 #' # check the Ensembl available biomart (if not known)
 #' # for Animals (host="www.ensembl.org", the default)
-#'  biomaRt::listEnsembl()
+#' biomaRt::listEnsembl()
 #'
 #' # List Ensembl available organisms
 #' Ensembl<-ViSEAGO::Ensembl2GO(
-#'  biomart="ensembl",
+#'  biomart="genes",
 #'  host="www.ensembl.org",
 #'  version=NULL
 #' )
 #' }
 #' @export
-Ensembl2GO=function(biomart="ensembl",host="www.ensembl.org",version=NULL){
+Ensembl2GO=function(biomart="genes",host="www.ensembl.org",version=NULL){
 
     # check the ensembl genes releases
     Ensembl<-listEnsembl(host=host,version=version)

README.md

@@ -27,7 +27,7 @@ remotes::install_gitlab(
     devtools::build("ViSEAGO")
 
     # install package (from R console)
-    install.packages("ViSEAGO_1.3.1.tar.gz", repos = NULL, type = "source")
+    install.packages("ViSEAGO_1.3.2.tar.gz", repos = NULL, type = "source")
 ```
 
 ## Citation

man/Ensembl2GO.Rd

@@ -4,10 +4,10 @@
 \alias{Ensembl2GO}
 \title{Check available organisms datasets at Ensembl.}
 \usage{
-Ensembl2GO(biomart = "ensembl", host = "www.ensembl.org", version = NULL)
+Ensembl2GO(biomart = "genes", host = "www.ensembl.org", version = NULL)
 }
 \arguments{
-\item{biomart}{the biomart name (eg. "ensembl", the default) available with \pkg{biomaRt} package \code{\link[biomaRt]{listEnsembl}}.}
+\item{biomart}{the biomart name (eg. "genes", the default) available with \pkg{biomaRt} package \code{\link[biomaRt]{listEnsembl}}.}
 
 \item{host}{the Ensembl host adress for \href{http://www.ensembl.org/index.html}{vertebrate} ("www.ensembl.org", the default value),
 \href{http://www.plants.ensembl.org/index.html}{plants} ("plants.ensembl.org"),
@@ -38,11 +38,11 @@ It uses the \code{\link[biomaRt]{useEnsembl}} and  \code{\link[biomaRt]{listData
 \dontrun{
 # check the Ensembl available biomart (if not known)
 # for Animals (host="www.ensembl.org", the default)
- biomaRt::listEnsembl()
+biomaRt::listEnsembl()
 
 # List Ensembl available organisms
 Ensembl<-ViSEAGO::Ensembl2GO(
- biomart="ensembl",
+ biomart="genes",
  host="www.ensembl.org",
  version=NULL
 )