[BioC] ChIPpeakAnno, getAnnotation question

[Zhu, Lihua (Julie)]

Neha,

Please use getAnnotation function in ChIPpeakAnno package to obtain the
annotation data you need. For detailed information on how to use
getAnnotation, please type help(getAnnotation) and let me know if this works
for you. Thanks!

Best regards,

Julie


On 9/20/13 8:56 AM, "Neha [guest]" <guest at bioconductor.org> wrote:

> 
> Hi Julie
> 
> 
> I am using ChIPpeakAnno for my data. The annotation data I would like to use
> Zebrafish but Zv9, though annotated data package has TSS.zebrafish.Zv8.
> I downloaded the "GTF"  file for Zv9 but I am unable to convert it into Ranged
> data using GFF2RangedData function since it accepts GFF file. Therefore, I am
> trying to make custom annotation using the following code.
> 
> 
> "
> 
> # create a biomart object and select a mart to use
> ensembl <- useDataset("drerio_gene_ensembl", mart=useMart("ensembl"))
> 
> # what kind of attributes can we retrieve?
> listAttributes(ensembl)
> 
> # set the properties to extract
> props <- c("ensembl_gene_id", "external_gene_id", "transcript_biotype",
> "chromosome_name", "start_position", "end_position", "strand")
> 
> # get the information
> genes <- getBM(attributes=props, mart=ensembl)
> 
> # create a RangedData object with my custom annotations
> myCustomAnno <- RangedData(IRanges(start=genes[,"start_position"],
> end=genes[,"end_position"], names=genes[,"ensembl_gene_id"]),
> space=genes[,"chromosome_name"], strand=genes[,"strand"])
> "
> 
> 
> But I am getting following error:
> 
> "Error in `rownames<-`(`*tmp*`, value = c("ENSDARG00000085528",
> "ENSDARG00000087771",  :
>   duplicate rownames not allowed"
> 
> I am unable to proceed ahead, also I very new in using this package. Could you
> suggest a solution.
> 
> 
> 
> Cheers,
> Neha
> 
>  -- output of sessionInfo():
> 
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] ChIPpeakAnno_2.2.0                  gplots_2.10.1
> KernSmooth_2.23-7                   caTools_1.12
>  [5] bitops_1.0-4.1                      gdata_2.8.2
> gtools_2.6.2                        limma_3.10.3
>  [9] org.Hs.eg.db_2.6.4                  GO.db_2.6.1
> RSQLite_0.11.1                      DBI_0.2-5
> [13] AnnotationDbi_1.16.19               BSgenome.Ecoli.NCBI.20080805_1.3.17
> BSgenome_1.22.0                     GenomicRanges_1.6.7
> [17] Biostrings_2.22.0                   IRanges_1.12.6
> multtest_2.10.0                     Biobase_2.14.0
> [21] biomaRt_2.10.0
> 
> loaded via a namespace (and not attached):
> [1] MASS_7.3-18      RCurl_1.91-1     splines_2.14.2   survival_2.36-14
> tools_2.14.2     XML_3.9-4
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor