Load gtf from local directory

[lmanchon]

--Hi,

is it possible to add a function in SCANVISannotation.R file to load annotation from local directory ?
Currently, it only uses an ftp connection to download a GTF file.

thank you --

[agiusp]

Sure thing, that's an easy adjustment - please try substituting lines 1-15 in the SCANVISannotation script with the lines below:

###################################
#INPUT: gtf.dir=dir where you have your gtf file

gtf.file=name of your gtf file

###################################
SCANVISannotation.provide_gtf
function (gtf.dir,gtf.file)
{
gencode <- rtracklayer::import.gff(file.path(gtf.dir, gtf.file), version = "2")

[lmanchon]

--
certainly, it's a way to do it and that's what I did.
It was also a suggestion I made to add this function to the package. This would avoid transfer by ftp.