Hi Hua,

Yes, I remember meeting you in CAMDA!

The insideFeature is set to TURE if the peak start is inside the gene
(between gene start and gene end). Positive (+) number for distancetoFeature
means the peak is inside or downstream of the gene. Negative (-) number for
distancetoFeature means the peak is upstream of the gene. Please note that
the distancetoFeature takes strand information into consideration already.

I suggest use peak summit as peak start so that the distancetoFeature is the
peak location to the transcription start site. Thanks!

Best regards,

Julie 


On 2/3/10 3:51 PM, "Li, Hua" <HUL@stowers.org> wrote:

> Julie:
>  
> This is Hua from Stowers Institute, we met in last year's CAMDA.
>  
> I am using you ChIPpeakAnno package, and have question about the
> "insideFeature".  Could you tell me what "+" and "-" number
> (distancetoFeature) means? And how do you decide which peak is TRUE for the
> "insideFeature".  I assume "insideFeature". Means if it close to a genes,
> right?
>  
> Thanks,
>  
> Hua
>  
> 


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