Commit ba4a144c authored by Aurelien Brionne's avatar Aurelien Brionne
Browse files

gen_table update

parent ba32286b
......@@ -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{
......
......@@ -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).
......
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