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(1543200,1557200,1563000,1569800,167889600,100,1000),
>     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
>
>
>
>

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