I'm trying to use rtracklayer's import function to import a GTF file. I downloaded the current comprehensive genome annotation for human from GENCODE, gunzipped the .gz file and tried the following:
library(rtracklayer) granges <-import("gencode.v36.annotation.gtf")
I am getting the following error:
Error in h(simpleError(msg, call)) : error in evaluating the argument 'con' in selecting a method for function 'import': invalid class “GFF2File” object: undefined class for slot "resource" ("characterORconnection")
Also, adding the parameter
format="gtf" does not make a difference.
When searching for this on the web, I'm only getting results regarding a tool called IsoformSwitchAnalyzeR where the authors recommended updating their software. But I'm neither using their tool, nor is it even installed on my PC.
For now, I am importing the GTF files manually, but I would like to use rtracklayer's import function. I hope, someone can help.