Question: ChIPpeakAnno, getAnnotation question
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5.6 years ago by
Neha Daga10
Neha Daga10 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@imls.uzh.ch Tel: +41 44 63 53153 (w) +41 786376748 (m) [[alternative HTML version deleted]]
modified 5.6 years ago by Julie Zhu4.0k • written 5.6 years ago by Neha Daga10
0
5.6 years ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:
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) > > > > > > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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