I am trying to create a function to extract the promoter regions from a gtf file only for "lincRNA" and "antisense" (under "type" column in the gtf file).
I think I need to start by using GenomicFeatures to first import the gtf file:
txdb = makeTxDbFromGFF("file.gtf", format="gtf")
But I don't think the column in the gtf file called "type" was imported.
How can I import and select the columns "lincRNA" and "antisense" from the TxDb file?
(Then I think would need to select only the exons and then the regions up and downstream by gene (which I think is done by the function "promoters" in GenomicRanges))