buil_genome_feature update par R3.5

R/build_genome_features.R

@@ -98,7 +98,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # convert to table
-    promoters_DT<-data.table::data.table(AnnotationDbi::as.data.frame(promoters))[,.(tx_id,tx_name)]
+    promoters_DT<-data.table::data.table(AnnotationDbi::as.data.frame(promoters,row.names = NULL))[,.(tx_id,tx_name)]
 
     ###################
     # convert to character
@@ -140,7 +140,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # convert to table
-    downstream_DT<-data.table::data.table(AnnotationDbi::as.data.frame(downstream))[,.(tx_id,tx_name)]
+    downstream_DT<-data.table::data.table(AnnotationDbi::as.data.frame(downstream,,row.names = NULL))[,.(tx_id,tx_name)]
 
     ###################
     # convert to character
@@ -181,7 +181,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # convert to table
-    UTR5_DT<-data.table::data.table(BiocGenerics::as.data.frame(UTR5))[,.(group_name,exon_rank)]
+    UTR5_DT<-data.table::data.table(BiocGenerics::as.data.frame(UTR5,,row.names = NULL))[,.(group_name,exon_rank)]
 
     ###################
     # convert to GRanges
@@ -217,7 +217,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # convert to table
-    UTR3_DT<-data.table::data.table(AnnotationDbi::as.data.frame(UTR3))[,.(group_name,exon_rank)]
+    UTR3_DT<-data.table::data.table(AnnotationDbi::as.data.frame(UTR3,,row.names = NULL))[,.(group_name,exon_rank)]
 
     ###################
     # convert to GRanges
@@ -253,7 +253,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # convert to table
-    exons_DT<-data.table::data.table(AnnotationDbi::as.data.frame(exons))[,.(group_name,exon_rank)]
+    exons_DT<-data.table::data.table(AnnotationDbi::as.data.frame(exons,row.names = NULL))[,.(group_name,exon_rank)]
 
     ###################
     # convert to GRanges
@@ -298,7 +298,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # convert to table
-    introns_DT<-data.table::data.table(AnnotationDbi::as.data.frame(introns))[,.(group_name,strand)]
+    introns_DT<-data.table::data.table(AnnotationDbi::as.data.frame(introns,row.names = NULL))[,.(group_name,strand)]
 
     ###################
     # convert to GRanges
@@ -352,7 +352,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
 
     ###################
     # convert to table
-    cds_DT<-data.table::data.table(AnnotationDbi::as.data.frame(cds))[,.(group_name,exon_rank)]
+    cds_DT<-data.table::data.table(AnnotationDbi::as.data.frame(cds,row.names = NULL))[,.(group_name,exon_rank)]
 
     ###################
     # convert to GRanges
@@ -412,9 +412,9 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
   # read the gff
   #gff<-data.table::fread(file,fill=T,drop=base::c(2,6,8),verbose=F,showProgress=F,col.names=base::c("chr",
   #"type","start","end","strand","att"))[data.table::like(type,"RNA|transcript") & !data.table::like(chr,"^#")]
-  
+
   gff<-data.table::fread(file,sep="",verbose=F,showProgress=F,header=F)[data.table::like(base::gsub("ID=.+$","",V1),"[[:space:]].+(RNA|transcript)"),]
-  
+
   ###################
   # parse it
   gff<-gff[,{