Hello Jianhong,

Thank you so much. It worked like a charm.

regards,
Alan




On Thu, Jul 18, 2013 at 3:04 PM, Ou, Jianhong <Jianhong.Ou@umassmed.edu>wrote:

> Hi Alan,
>
> I think one way is that to create object Granges first and then convert it
> to RangedData use code like,
>
> exons <- exons(TranscriptDb, columns=NULL)
>     introns <- unique(unlist(intronsByTranscript(TranscriptDb)))
>     fiveUTRs <- unique(unlist(fiveUTRsByTranscript(TranscriptDb)))
>     threeUTRs <- unique(unlist(threeUTRsByTranscript(TranscriptDb)))
>     transcripts <- transcripts(TranscriptDb, columns=NULL)
>
>
> Hope this will help you.
>
> Yours sincerely,
>
> Jianhong Ou
>
> LRB 670A
> Program in Gene Function and Expression
> 364 Plantation Street Worcester,
> MA 01605
>
>
>
>
> On 7/18/13 3:39 PM, "Alan Smith" <alan.sm310@gmail.com> wrote:
>
> >Hello All,
> >
> >I apologize if this email shows up twice to the mailing list.
> >
> >I'm trying to use ChIPpeakAnno to identify the annotation of ChIP-Seq
> >peaks
> >for an organism that does not have an annotation package. I have used
> >makeTranscriptDbFromGFF to create a transcriptDb object and trying to pass
> >it as the annotation data for annotatePeakInBatch function. However, I
> >suppose it is not the way to handle that. I tried googling quite a bit but
> >no luck.
> >
> >Is there a way to convert TranscriptDb object to RangedData?
> >
> >The error I ended up with:
> >
> >Error in annotatePeakInBatch(t.rangedData, AnnotationData = ep,  :
> >  AnnotationData needs to be RangedData object
> >
> >Please let me know how to approach this issue.
> >Thanks for any help.
> >Alan
> >
> >Here is my code and sessionInfo:
> >
> >library(ChIPpeakAnno)
> >test.rangedData = BED2RangedData("ChIP-test.bed")
> >test.rangedData
> >txdb <- makeTranscriptDbFromGFF(file="spgen.gtf", format="gtf",
> >exonRankAttributeName="exon_number", dataSource=paste("eunam",sep=""),
> >species="epp")
> >saveDb(txdb,file="spgenGTF.sqlite")
> >ep <- loadDb("spgenGTF.sqlite",)
> >annotatedPeakEP= annotatePeakInBatch(test.rangedData, AnnotationData = ep,
> >output="both", maxgap=1000, multiple=TRUE)
> >
> >Error in annotatePeakInBatch(test.rangedData, AnnotationData = ep,  :
> >  AnnotationData needs to be RangedData object
> >
> >sessionInfo()
> >R version 3.0.1 (2013-05-16)
> >Platform: x86_64-apple-darwin10.8.0 (64-bit)
> >
> >locale:
> >[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> >attached base packages:
> >[1] parallel  grid      stats     graphics  grDevices utils     datasets
> > methods   base
> >
> >other attached packages:
> > [1] rtracklayer_1.20.4                  ChIPpeakAnno_2.8.0
> > GenomicFeatures_1.12.2              limma_3.16.6
> > [5] org.Hs.eg.db_2.9.0                  GO.db_2.9.0
> >  RSQLite_0.11.4                      DBI_0.2-7
> > [9] AnnotationDbi_1.22.6
> > BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.28.0
> >GenomicRanges_1.12.4
> >[13] Biostrings_2.28.0                   IRanges_1.18.2
> > multtest_2.16.0                     Biobase_2.20.1
> >[17] biomaRt_2.16.0                      BiocGenerics_0.6.0
> > VennDiagram_1.6.0
> >
> >loaded via a namespace (and not attached):
> > [1] bitops_1.0-5     MASS_7.3-27      RCurl_1.95-4.1   Rsamtools_1.12.3
> >splines_3.0.1    stats4_3.0.1     survival_2.37-4  tools_3.0.1
> > [9] XML_3.95-0.2     zlibbioc_1.6.0
> >
> >       [[alternative HTML version deleted]]
> >
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>

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