[BioC] Question about ChIPpeakAnno R package: peakNearBDP
Zhu, Lihua (Julie)
Julie.Zhu at umassmed.edu
Wed Aug 8 04:50:30 CEST 2012
The bug has been fixed. Please download ChIPpeakAnno 2.5.11 if you need to
set PeakLocForDistance and/or FeatureLocForDistance in peaksNearBDP.
Thanks again for your feedback!
On 8/7/12 11:25 AM, "Lihua Julie Zhu" <julie.zhu at umassmed.edu> wrote:
> 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,
> On 8/7/12 10:51 AM, "EYBOULET Fanny 228361" <fanny.eyboulet at cea.fr> wrote:
> I‚m using ChIPpeakAnno 2.4.0 to annotate my peaks after peakcalling with
> 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 =
> minus = annotatePeakInBatch(myPeakList, AnnotationData = AnnoMinus)
> Is there an explanation for this difference ? Or is it a mistake?
> Thanks in advance for your answer.
> Fanny Eyboulet
> PhD student
> Bat. 144 CEA Saclay
> 91191 Gif sur Yvette Cedex France
> Tel : 0169086125
> @ : fanny.eyboulet at cea.fr
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