[BioC] ChIPpeakAnno, getAnnotation question

[Zhu, Lihua (Julie)]

Neha,

Did you get my earlier response? For your convenience, here it is again.

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).

Also, you could change your code slightly to:

myCustomAnno <- RangedData(IRanges(start=genes[,"start_position"],
end=genes[,"end_position"], names=paste(genes[,"ensembl_gene_id"],
genes[,"start_position"],sep="-")),
 space=genes[,"chromosome_name"], strand=genes[,"strand"])

Please let me know if this works for you. Thanks!

Best regards,

Julie



On 9/20/13 8:43 AM, "Neha Daga" <neha.daga at imls.uzh.ch> 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
> 
> 
> 
> 
> 
> 
> 
>                  
> Neha Daga
> Bioinformatics Group ( Prof. Von Mering)
> Institute of Molecular Life Sciences
> Winterthurerstrasse 190
> CH-8057 Zurich
> Switzerland
> neha.daga at imls.uzh.ch
> Tel: +41 44 63 53153 (w)
>         +41 786376748   (m)
>                  
> 
> 
> 
> 
> 
> 
> 
> 
> 
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> 
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