I believe that the annotation you obtained from different resources
are different versions, e.g.,mm10 from Ensemble.
I am travelling today. Jianhong will be happy to help you. If you
could keep the thread in the bioconductor list for others to
contribute/benefit, that would be very much appreciated. Thanks!
On 12/11/12 2:49 PM, "Holly" <email@example.com> wrote:
One more question is about how to annotation of intron peaks. I
appreciate if you could test the following example and help to figure
out how to correctly annotate it using ChIPpeakAnno.
For example, I ran the following codes based on the updated
rd <- RangedData(IRanges(start = 37377492, end= 37378857) ,
annotatePeakInBatch(rd, AnnotationData = TSS.mouse.NCBIM37)
Then I got a result as following:
RangedData with 1 row and 9 value columns across 1 space
space ranges | peak
<factor> <iranges> | <character>
1 ENSMUSG00000073593 18 [37377492, 37378857] | 1
feature start_position end_position
<character> <numeric> <numeric>
1 ENSMUSG00000073593 ENSMUSG00000073593 37319509 37338176
insideFeature distancetoFeature shortestDistance
<character> <numeric> <numeric>
1 ENSMUSG00000073593 upstream -39316 39316
1 ENSMUSG00000073593 NearestStart
However, on GenomeBrowser http://genome.ucsc.edu/cgi-bin/hgTracks
(MCBI37/mm9), it is an intron region of gene Pcdha4-9.
While if I am trying:
annotatePeakInBatch(rd, AnnotationData = Annotation)
it gives a totally different results as ENSMUSG00000051242 which is
also not as I expected.
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)
attached base packages:
 grid stats graphics grDevices utils datasets
other attached packages:
 org.Mm.eg.db_2.8.0 ChIPpeakAnno_2.6.0
 limma_3.14.3 org.Hs.eg.db_2.8.0
 GO.db_2.8.0 RSQLite_0.11.2
 BSgenome_1.26.1 Biostrings_2.26.2
 multtest_2.14.0 biomaRt_2.14.0
 VennDiagram_1.5.1 BayesPeak_1.10.0
 rtracklayer_1.18.1 GenomicFeatures_1.10.1
 AnnotationDbi_1.20.3 Biobase_2.18.0
 GenomicRanges_1.10.5 IRanges_1.16.4
 BiocGenerics_0.4.0 BiocInstaller_1.8.3
loaded via a namespace (and not attached):
 bitops_1.0-5 MASS_7.3-22 parallel_2.15.2 RCurl_1.95-3
 Rsamtools_1.10.2 splines_2.15.2 stats4_2.15.2
 tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0
On 12/10/2012 01:10 PM, Zhu, Lihua (Julie) wrote:
Thanks for the link! The BDPs in ChIPpeakAnno is defined purely
the coordinates of known genes.
On 12/10/12 1:30 PM, "Holly" <firstname.lastname@example.org>
A basic question to verify your definition of the bi-directional
did you define them purely according to the coordinates of known
have you referred to the experimental data, e.g. EST experiments done
I learned a lot from the discussion with you. Thanks again,
On 12/10/2012 10:46 AM, Zhu, Lihua (Julie) wrote:
I believe that you are interested in finding the peaks that reside in
bi-directional promoters. If so, you can use the following functions
BDP = peaksNearBDP(peaks, AnnotationData=TSS, MaxDistance =5000)
c(BDP$percentPeaksWithBDP, BDP$n.peaksWithBDP, BDP$n.peaks)
all.genes = union(annotated.peaks$feature, BDP$peaksWithBDP$feature)
where annotated.peaks is generated from annotatePeakInBatch using TSS.
learn more about peaksNearBDP, please type ?peaksNearBDP in R.
If you just want to find genes on both side of the peaks within
distance away from the peaks, you can use the following command.
Annotated.peaks = annotatePeakInBatch(peaks, AnnotationData = TSS,
Where maxgap can be adjusted according to your needs.
Please let me know if this suits your needs. Thanks!
On 12/10/12 11:19 AM, "Holly" <email@example.com>
I am trying to annotate peaks for not only the genes with the nearest
TSS but the ones at the other side of the peaks.
Do you think I can use ChIPpeakAnno to get both sided genes for a peak
region? If so, what do you suggest?
Thanks a lot,
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