Commit 7ad710a3 authored by Aurelien Brionne's avatar Aurelien Brionne
Browse files

buil_genome_feature update par R3.5

parent 84cd943e
...@@ -98,7 +98,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters) ...@@ -98,7 +98,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
################### ###################
# convert to table # 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 # convert to character
...@@ -140,7 +140,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters) ...@@ -140,7 +140,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
################### ###################
# convert to table # 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 # convert to character
...@@ -181,7 +181,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters) ...@@ -181,7 +181,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
################### ###################
# convert to table # 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 # convert to GRanges
...@@ -217,7 +217,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters) ...@@ -217,7 +217,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
################### ###################
# convert to table # 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 # convert to GRanges
...@@ -253,7 +253,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters) ...@@ -253,7 +253,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
################### ###################
# convert to table # 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 # convert to GRanges
...@@ -298,7 +298,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters) ...@@ -298,7 +298,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
################### ###################
# convert to table # 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 # convert to GRanges
...@@ -352,7 +352,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters) ...@@ -352,7 +352,7 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
################### ###################
# convert to table # 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 # convert to GRanges
...@@ -412,9 +412,9 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters) ...@@ -412,9 +412,9 @@ setMethod("build_genome_features",definition=function(txdb,features,parameters)
# read the gff # 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", #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,"^#")] #"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=.+$","",V1),"[[:space:]].+(RNA|transcript)"),] gff<-data.table::fread(file,sep="",verbose=F,showProgress=F,header=F)[data.table::like(base::gsub("ID=.+$","",V1),"[[:space:]].+(RNA|transcript)"),]
################### ###################
# parse it # parse it
gff<-gff[,{ gff<-gff[,{
......
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