promoter definition in VariantAnnotation
1
0
Entering edit mode
lidia.mateo ▴ 30
@lidiamateo-7243
Last seen 13 months ago
Spain

Hi!

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)?

Lídia

2
Entering edit mode
@valerie-obenchain-4275
Last seen 22 months ago
United States

Hi Lidia,

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()’ ...

Default values:

> PromoterVariants()
class: PromoterVariants
upstream: 2000
downstream: 200 

Defaults can be changed to fit your use case.

> PromoterVariants(upstream = 5000)
class: PromoterVariants
upstream: 5000
downstream: 200 

Valerie

0
Entering edit mode

Hi Valerie,

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!

Lidia