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@imls.uzh.ch
Tel: +41 44 63 53153 (w)
        +41 786376748   (m)
                                                               









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