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Question: Question about the ChIPpeakAnno:
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gravatar for Julie Zhu
3.3 years ago by
Julie Zhu3.6k
United States
Julie Zhu3.6k 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(1543200,1557200,1563000,1569800,16 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]]
ADD COMMENTlink modified 6 weeks ago by jinj0 • written 3.3 years ago by Julie Zhu3.6k
0
gravatar for BH Tang
3.3 years ago by
BH Tang20
BH Tang20 wrote:
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]]
ADD COMMENTlink written 3.3 years ago by BH Tang20
0
gravatar for jinj
6 weeks ago by
jinj0
jinj0 wrote:

Hi,everyone

i also have a question when i do the peakannotation.

4: getGenomicAnnotation.internal(peaks, genomicRegion, type, sameStrand = sameStrand)
3: updateGenomicAnnotation(peaks, intronList, "Intron", anno, sameStrand = sameStrand)
2: getGenomicAnnotationpeak.gr, distance, tssRegion, TxDb, level, 
       genomicAnnotationPriority, sameStrand = sameStrand)
1: annotatePeak(a, tssRegion = c(-3000, 3000), TxDb = txdb)
> peakAnno <- annotatePeak(a,tssRegion=c(-3000, 3000), TxDb=txdb)
>> loading peak file...                          2017-06-08 11:03:18 
>> preparing features information...             2017-06-08 11:03:18 
>> identifying nearest features...               2017-06-08 11:03:18 
>> calculating distance from peak to TSS...      2017-06-08 11:03:18 
>> assigning genomic annotation...               2017-06-08 11:03:18 
Error in `[[<-`(`*tmp*`, name, value = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,  : 
  76282 elements in value to replace 150594 elements
此外: Warning message:
In .Seqinfo.mergexy(x, y) :
  Each of the 2 combined objects has sequence levels not in the other:
  - in 'x': AC156495, AC160949, AP008246, AP008247, Syng_TIGR_007, Syng_TIGR_009, Syng_TIGR_012, Syng_TIGR_022, Syng_TIGR_024, Syng_TIGR_031, Syng_TIGR_033, Syng_TIGR_036, Syng_TIGR_038
  - in 'y': chrNA
  Make sure to always combine/compare objects based on the same reference
  genome (use suppressWarnings() to suppress this warning).

ADD COMMENTlink written 6 weeks ago by jinj0

this is my installed R package,my friend also installed this package and analysis the same bed and txdb,It work. I don't know why ?

 

ADD REPLYlink modified 5 weeks ago • written 6 weeks ago by jinj0
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