Ben, Thanks for the email! AnnotatePeakInBatch has quite a few parameter to set other than default setting. Depending on how you use it and your purpose, you could get different kind of annotation done including stranded annotation. ChIPseq and ChIPchip protocol are strandless, meaning that you cannot distinguish peaks in + strand or – strand. However, for other type of experiments such as Aseq for example, peaks have strand information. For stranded annotation, please do the following. data(TSS.human.NCBI36) PlusAnno = TSS.human.NCBI36[strand(TSS.human.NCBI36) == "+" | strand(TSS.human.NCBI36) == "1",] MinusAnno = TSS.human.NCBI36[strand(TSS.human.NCBI36) == "-" | strand(TSS.human.NCBI36) == "-1",] myexp = RangedData(IRanges(start=c(1543200,1557200,1563000,1569800,16 7889600,100,1000), end=c(1555199,1560599,1565199,1573799,167893599,200,1200), names=c("p1","p2","p3","p4","p5","p6", "p7")), strand=c("+" ,"-" ,"+" ,"+" ,"+" ,"+" ,"-" ), space=c(6,6,6,6,5,4,4)) Plus.annotatedPeak = annotatePeakInBatch(myexp[strand(myexp)== "+" ,] , AnnotationData = PlusAnno) Minus.annotatedPeak = annotatePeakInBatch(myexp[strand(myexp)== "-" ,] , AnnotationData = MinusAnno) as.data.frame(Plus.annotatedPeak) as.data.frame(Minus.annotatedPeak) Hope this helps! Please feel free to contact me if you need further clarification or encounter any problem. I would appreciate if you could cc Bioncondutor list to benefit others who might have similar issues. Best regards, Julie On 4/18/14 9:18 AM, "BH Tang" <glad.tang@gmail.com> wrote: Hi Julie, YGC posted his comments and revision on your ChIP peak annotation package; they said your package does not consider the strand information, see the below two links: http://ygc.name/2014/01/14/bug-of-r-package-chippeakanno/ http://ygc.name/2014/04/13/chipseeker-for-chip-peak-annotation/ How do you think of it? Since I am also using your ChIPpeakAnno package, I am very curious about its reliability and robustness. Thanks a lot for your work. -Ben [[alternative HTML version deleted]]

Thanks a lot for your quick reply, Julie, I'll check into the question further. Best regards. -Ben On Fri, Apr 18, 2014 at 10:23 AM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: > Ben, > > Thanks for the email! > > AnnotatePeakInBatch has quite a few parameter to set other than default > setting. Depending on how you use it and your purpose, you could get > different kind of annotation done including stranded annotation. > > ChIPseq and ChIPchip protocol are strandless, meaning that you cannot > distinguish peaks in + strand or – strand. However, for other type of > experiments such as Aseq for example, peaks have strand information. > > For stranded annotation, please do the following. > > data(TSS.human.NCBI36) > PlusAnno = TSS.human.NCBI36[strand(TSS.human.NCBI36) == "+" | > strand(TSS.human.NCBI36) == "1",] > MinusAnno = TSS.human.NCBI36[strand(TSS.human.NCBI36) == "-" | > strand(TSS.human.NCBI36) == "-1",] > > > myexp = > RangedData(IRanges(start=c(1543200,1557200,1563000,1569800,16788960 0,100,1000), > end=c(1555199,1560599,1565199,1573799,167893599,200,1200), > names=c("p1","p2","p3","p4","p5","p6", "p7")), strand=c("+" ,"-" ,"+" ,"+" > ,"+" ,"+" ,"-" ), space=c(6,6,6,6,5,4,4)) > > > Plus.annotatedPeak = annotatePeakInBatch(myexp[strand(myexp)== "+" ,] , > AnnotationData = PlusAnno) > > Minus.annotatedPeak = annotatePeakInBatch(myexp[strand(myexp)== "-" ,] , > AnnotationData = MinusAnno) > > > as.data.frame(Plus.annotatedPeak) > > as.data.frame(Minus.annotatedPeak) > > > Hope this helps! Please feel free to contact me if you need further > clarification or encounter any problem. I would appreciate if you could cc > Bioncondutor list to benefit others who might have similar issues. > > Best regards, > > Julie > > > On 4/18/14 9:18 AM, "BH Tang" <glad.tang@gmail.com> wrote: > > Hi Julie, > > YGC posted his comments and revision on your ChIP peak annotation package; > they said your package does not consider the strand information, see the > below two links: > > http://ygc.name/2014/01/14/bug-of-r-package-chippeakanno/ > http://ygc.name/2014/04/13/chipseeker-for-chip-peak-annotation/ > > How do you think of it? Since I am also using your ChIPpeakAnno package, I > am very curious about its reliability and robustness. > > Thanks a lot for your work. > > -Ben > > > > [[alternative HTML version deleted]]