I am using VariantAnnotation package to functionally annotate a VCF file in Drosophila melanogaster. I could not find in the documentation the promoter definition. Is it a region of a fixed length located 5' from the transcription start site? or is it a genomic feature that is annotated in the corresponding package (e.g. TxDb object)?
I'm guessing you're using locateVariants() and are wondering about the PromoterVariants() class.
The man page for locateVariants defines the promoter region as up/down stream of the transcription start site:
‘promoter’ variants fall within a specified range upstream
and downstream of the transcription start site. Ranges values
can be set with the ‘upstream’ and ‘downstream’ arguments
when creating ‘PromoterVariants()’ ...
Thank you very much for your answer! it is exactly what I needed to know. I was using locateVariants() with default arguments but I see that using the specific classes is even better!