Question: biomRt package to get the 3'utr sequences of refseq predicted genes
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gravatar for Harpreet Saini
11.1 years ago by
United Kingdom
Harpreet Saini30 wrote:
Hi, I am getting some problem in using 'BiomaRt' package to obtain the 3' UTR sequences of refseq predicted genes. I am using the following command: > getSequence (id=refseqID,type="refseq_dna_predicted",seqType="3utr",mart=ensembl), where refseqId is a list of my refseq predicted genes. I am getting the following error: Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, : Invalid attribute(s): refseq_dna_predicted I checked the filters and attributes also to confirm if the type is alright. It seems that the type should be 'refseq_dna_predicted'. Any help would be great. sessionInfo() > sessionInfo() R version 2.7.2 (2008-08-25) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.4.5 Biobase_2.0.1 limma_2.14.6 biomaRt_1.14.1 RCurl_0.9-4 loaded via a namespace (and not attached): [1] XML_1.96-0 Thanks Harpreet Harpreet Kaur Saini Enright Group EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Tel: +44-(0) 1223-492676
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ADD COMMENTlink modified 11.1 years ago by steffen@stat.Berkeley.EDU600 • written 11.1 years ago by Harpreet Saini30
Answer: biomRt package to get the 3'utr sequences of refseq predicted genes
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gravatar for steffen@stat.Berkeley.EDU
11.1 years ago by
Hi Harpreet, Thanks for reporting this. getSequence is a wrapper function that makes thing easy to retrieve but it expect certain things such as that the used filter is also an attribute that is retrievable. In this case refseq_dna_predicted is given as filter but the corresponding attribute is refseq_DNA_predicted so these are not the same and this makes your query fail. I'll investigate this mismatch and try to fix it. In the meantime you could do your query: getBM(c("ensembl_gene_id","3utr"), filters= "refseq_dna_predicted", values = "XM_940223", mart = ensembl) This should work. Cheers, Steffen > Hi, > > I am getting some problem in using 'BiomaRt' package to obtain the 3' > UTR sequences of refseq predicted genes. I am using the following > command: > > > getSequence > (id=refseqID,type="refseq_dna_predicted",seqType="3utr",mart=ensembl), > where refseqId is a list of my refseq predicted genes. > > I am getting the following error: > > Error in getBM(c(seqType, type), filters = type, values = id, mart = > mart, : > Invalid attribute(s): refseq_dna_predicted > > I checked the filters and attributes also to confirm if the type is > alright. It seems that the type should be 'refseq_dna_predicted'. > > Any help would be great. > > sessionInfo() > > sessionInfo() > R version 2.7.2 (2008-08-25) > i386-apple-darwin8.11.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] GEOquery_2.4.5 Biobase_2.0.1 limma_2.14.6 biomaRt_1.14.1 > RCurl_0.9-4 > > loaded via a namespace (and not attached): > [1] XML_1.96-0 > > > Thanks > Harpreet > Harpreet Kaur Saini > Enright Group > EMBL-European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > Tel: +44-(0) 1223-492676 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 11.1 years ago by steffen@stat.Berkeley.EDU600
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