gen_table update

R/build_genome_features.R

@@ -388,7 +388,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
   }
 
   ###################
-  # load annotation supplement
+  # load annotation complement
   ###################
 
     ###################
@@ -434,7 +434,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
         ###################
         # select columns from gtf
         gene_table<-gene_table[,
-          .(seqnames,start,end,strand,type,gene_id,gene_name,gene_biotype,transcript_id)
+          .(seqnames,start,end,strand,type,gene_name,transcript_id,gene_id)
         ]
 
       }else{
@@ -448,12 +448,14 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
         ###################
         # extract gene_id
         gene_table[,
-          `:=`(
-          gene_id=base::sub("^.+:","",Dbxref[[1]][1]),
-          Dbxref=NULL
-          ),
+          gene_id:=base::sub("^.+:","",Dbxref[[1]][1]),
           by=1:base::nrow(gene_table)
-        ]
+        ][,Dbxref:=NULL]
+
+        ###################
+        # reneme gene to gene_name
+        base::names(gene_table)[6]<-"gene_name"
+
       }
 
   }else{

vignettes/introduction.Rmd

@@ -94,6 +94,34 @@ toplevel=GenomicFeatures::makeTxDbFromGFF(
   taxonomyId=9031,
   dbxrefTag="ID"
 )
+
+toplevel=GenomicFeatures::makeTxDbFromGFF(
+  file=file,
+  format="gff",
+  organism="Gallus gallus",
+  taxonomyId=9031,
+  dbxrefTag="ID"
+)
+
+
+
+file="/home/abrionne/Documents/SAVE_uraanabioinfo/programmes_R/GenomeFeatures/inst/extdata/data/input/galGal5.gff"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
 ```
 
 Now, we build a convenient object with `GenomeFeatures::build_genome_features`, needed for find overlaps beetween all selected features and genomic coordinates targets into a single step (see below).