Hi Dario,

Could you please send your code snippets and session info? Thanks!

Best regards,

Julie


On 5/14/10 1:48 AM, "Dario Strbenac" <D.Strbenac@garvan.org.au> wrote:

Hello,

It seems that the annotatePeakInBatch function completely ignores strand information :

> peaks
RangedData with 3 rows and 1 value column across 1 space
        space       ranges |   strand
  <character>    <IRanges> | <factor>
1        chr1 [1000, 2000] |        +
2        chr1 [2000, 3000] |        +
3        chr1 [3000, 4000] |        +
> features
RangedData with 3 rows and 1 value column across 1 space
        space       ranges |   strand
  <character>    <IRanges> | <factor>
1        chr1 [1500, 2500] |        -
2        chr1 [2500, 3500] |        -
3        chr1 [3500, 4500] |        -
> annotatePeakInBatch(peaks, AnnotationData = features)
RangedData with 3 rows and 9 value columns across 1 space
          space       ranges |        peak      strand     feature start_position end_position insideFeature distancetoFeature shortestDistance fromOverlappingOrNearest
    <character>    <IRanges> | <character> <character> <character>      <numeric>    <numeric>   <character>         <numeric>        <numeric>              <character>
1 1        chr1 [1000, 2000] |           1           1           1           1500         2500  overlapStart              -500              500             NearestStart
2 1        chr1 [2000, 3000] |           2           1           1           1500         2500    overlapEnd               500              500             NearestStart
3 2        chr1 [3000, 4000] |           3           1           2           2500         3500    overlapEnd               500              500             NearestStart

Shouldn't get anything overlapping ...

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia

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