[BioC] Distance to Feature

[Sarah Sheppard]

It would seem that this function does not account for strand then.  For example, for this peak the  "distance to feature" is given as -7364 

The output line is this:

"38163"	"20"	39614606	39614683	78	"56822 ENSDART00000023531"	"56822"	"-"	"ENSDART00000023531"	39614524	39622047	"inside"	-7364	82	"Overlapping"

The ensembl annotation in my bed file is this: 

20 39614524 39622047 ENSDART00000023531 1 -1

Note these are both on the minus strand, so the end coordinate would be the left most coordinate, so end of the peak to the end of the feature would be  39614606 -39614524 = 82
Instead, AnnotatePeakInBatch calculates this as the right most coordinates e.g.   rightmost peak coordinate 39614683- rightmost transcript coordinate (really the start here)39622047= -7364

Am I doing something wrong? or do I need to change the source code somehow?

Thanks,
Sarah
On Mar 1, 2011, at 1:52 PM, Zhu, Lihua (Julie) wrote:

> Sarah,
> 
> Yes, your assumption is correct.
> 
> Best regards,
> 
> Julie
> 
> 
> On 3/1/11 1:50 PM, "Sarah Sheppard" <SarahSheppard at gmail.com> wrote:
> 
>> Hi Julie,
>> 
>> 
>> 
>> I thought when specifying "FeatureLocForDistance" as "end" and
>> "PeakLocForDistance" as "end", that I would get the distance from the end of
>> the peak (Rmost coord on the + strand, Lmost coord. on the - strand) to the
>> end of the feature (e.g. transcript, since these are the coordinates I used in
>> the annotation data) in "distance to feature". In the "distance to feature"
>> output description, it says "distance to nearest feature, such as tss".
>> 
>> Am I incorrect in my assumption of what value is expressed in "distance to
>> feature"?
>> 
>> Thanks,
>> Sarah
> 
>