Question: ChIPpeakAnno, getAnnotation question
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6.2 years ago by
Guest User12k
Guest User12k 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.
ADD COMMENTlink modified 6.2 years ago by Julie Zhu4.1k • written 6.2 years ago by Guest User12k
Answer: ChIPpeakAnno, getAnnotation question
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gravatar for Julie Zhu
6.2 years ago by
Julie Zhu4.1k
United States
Julie Zhu4.1k wrote:
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
ADD COMMENTlink written 6.2 years ago by Julie Zhu4.1k
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