[BioC] ChIPpeakAnno, getAnnotation question

[Neha [guest]]

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       

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