Question about ChIPpeakAnno R package
1
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
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 [[alternative HTML version deleted]]
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno • 597 views
ADD COMMENT
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
Fanny, 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! Best regards, Julie On 8/7/12 11:25 AM, "Lihua Julie Zhu" <julie.zhu at="" umassmed.edu=""> wrote: > 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 at="" 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 at cea.fr > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENT

Login before adding your answer.

Traffic: 179 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6