merge_enrich_terms update for Ensembl

DESCRIPTION

 Package: ViSEAGO
-Version: 1.7.2
+Version: 1.7.3
 Title: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
 Author: Aurelien Brionne [aut, cre],
         Amelie Juanchich [aut],

R/Ensembl2GO.R

@@ -3,6 +3,7 @@
 #' @importFrom biomaRt useEnsembl listEnsembl listEnsemblGenomes useEnsemblGenomes listDatasets 
 #' @importFrom data.table data.table
 #' @param biomart the biomart name available with \pkg{biomaRt} package \code{\link[biomaRt]{listEnsembl}} ("genes", the default) or \code{\link[biomaRt]{listEnsemblGenomes}} ("protists_mart", "fungi_mart", "plants_mart").
+#' @param GRCh GRCh version to connect to if not the current GRCh38, currently this can only be 37
 #' @param version the annotation version to use (eg. NULL for the default current version, or a version number in \code{character})
 #' @family genomic_ressource
 #' @details
@@ -27,11 +28,12 @@
 #' # List Ensembl available organisms
 #' Ensembl<-ViSEAGO::Ensembl2GO(
 #'  biomart="genes",
+#'  GRCh = NULL,
 #'  version=NULL
 #' )
 #' }
 #' @export
-Ensembl2GO=function(biomart="genes",version=NULL){
+Ensembl2GO=function(biomart="genes",GRCh = NULL,version=NULL){
 
     # check the ensembl host versus mart name
     match.arg(biomart,c("genes","protists_mart","fungi_mart","metazoa_mart","plants_mart"))
@@ -40,10 +42,17 @@ Ensembl2GO=function(biomart="genes",version=NULL){
     if(biomart=="genes"){
 
         # check the ensembl genes releases
-        Ensembl<-listEnsembl(version=version)
+        Ensembl<-listEnsembl(
+            GRCh =GRCh,
+            version=version
+        )
 
         # connect to Ensembl
-        mart<-useEnsembl(biomart,version=version)
+        mart<-useEnsembl(
+            biomart,
+            GRCh =GRCh,
+            version=version
+        )
 
     }else{
 
@@ -58,7 +67,7 @@ Ensembl2GO=function(biomart="genes",version=NULL){
     new(
         "genomic_ressource",
         db="Ensembl",
-        stamp=paste(biomart,Ensembl$version[Ensembl$biomart==biomart]),
+        stamp=paste(biomart,GRCh,Ensembl$version[Ensembl$biomart==biomart]),
         data=data.table(),
         mart=list(mart),
         organisms=data.table(listDatasets(mart))

R/merge_enrich_terms.R

@@ -493,21 +493,31 @@ setMethod(
             # if db  match to Ensembl
             if(db[1]=="Ensembl"){
 
-                if(db[3]!="http://grch37.ensembl.org"){
+                if(db[4]==""){
 
-                    # connect to Ensembl
-                    mart<-useEnsembl(
-                        biomart="genes",
-                        host=db[3],
-                        version=db[6]
-                    )
+                    # Connect to Ensembl
+                    if(db[3]=="genes"){
 
+                        # connect to Ensembl
+                        mart<-useEnsembl(
+                            biomart=db[3],
+                            version=tail(db,n=1)
+                            
+                        )
+                        
+                    }else{
+
+                        # connect to Ensembl
+                        mart<-useEnsemblGenomes(
+                            biomart=db[3]
+                        )
+                    }
                 }else{
                     # connect to Ensembl
                     mart<-useEnsembl(
                         biomart="genes",
-                        GRCh =37,
-                        version=db[6]
+                        GRCh =db[4],
+                        version=tail(db,n=1)
                     )
                 }
 

README.md

@@ -27,7 +27,7 @@ remotes::install_gitlab(
     devtools::build("ViSEAGO")
 
     # install package (from R console)
-    install.packages("ViSEAGO_1.7.1.tar.gz", repos = NULL, type = "source")
+    install.packages("ViSEAGO_1.7.3.tar.gz", repos = NULL, type = "source")
 ```
 
 ## Citation

man/Ensembl2GO.Rd

@@ -4,11 +4,13 @@
 \alias{Ensembl2GO}
 \title{Check available organisms datasets at Ensembl.}
 \usage{
-Ensembl2GO(biomart = "genes", version = NULL)
+Ensembl2GO(biomart = "genes", GRCh = NULL, version = NULL)
 }
 \arguments{
 \item{biomart}{the biomart name available with \pkg{biomaRt} package \code{\link[biomaRt]{listEnsembl}} ("genes", the default) or \code{\link[biomaRt]{listEnsemblGenomes}} ("protists_mart", "fungi_mart", "plants_mart").}
 
+\item{GRCh}{GRCh version to connect to if not the current GRCh38, currently this can only be 37}
+
 \item{version}{the annotation version to use (eg. NULL for the default current version, or a version number in \code{character})}
 }
 \value{
@@ -29,6 +31,7 @@ biomaRt::listEnsembl()
 # List Ensembl available organisms
 Ensembl<-ViSEAGO::Ensembl2GO(
  biomart="genes",
+ GRCh = NULL,
  version=NULL
 )
 }