Fanny,

Thanks for the feedback! Yes, it is a mistake. If you use the default setting of peaksNearBDP, then it will not affect the results. I will update the dev version and keep you updated.

Best regards,

Julie


On 8/7/12 10:51 AM, "EYBOULET Fanny 228361" <fanny.eyboulet@cea.fr> wrote:

Hello,
I’m using ChIPpeakAnno 2.4.0 to annotate my peaks after peakcalling with Bayespeak.
There is no problem when I use the command annotatePeakInBatch but I have a question about the command peaksNearBDP. When I looked a little closer to the script, I noticed that the peaklocfordistance is not calculated the same way for plus and minus annotations. Here are the lines I’m talking about :
plus = annotatePeakInBatch(myPeakList, AnnotationData = AnnoPlus,
        PeakLocForDistance = PeakLocForDistance, FeatureLocForDistance = FeatureLocForDistance)
minus = annotatePeakInBatch(myPeakList, AnnotationData = AnnoMinus)
Is there an explanation for this difference ? Or is it a mistake?
Thanks in advance for your answer.
Sincerely.



Fanny Eyboulet
PhD student
DSV/iBiTec-s/SBIGeM/LREGE
Bat. 144 CEA Saclay
91191 Gif sur Yvette Cedex France
Tel : 0169086125
@ : fanny.eyboulet@cea.fr



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