promoter definition in VariantAnnotation
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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)?

Thank you for your time,

Lídia

VariantAnnotation promoter drosophila melanogaster • 937 views
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@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 

If this does not answer your question please try again, maybe with a code example.

Valerie

 

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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

 

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