Error in makeGeneRegion from GenomeGraphs
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Mark Dunning ★ 1.1k
@mark-dunning-3319
Last seen 20 months ago
Sheffield, Uk
Hi all, I am trying to use the makeGeneRegion function in GenomeGraphs to get the locations of exons within a particular genomic region. The function seems to take an extraordinarily long time and then returns an error. >mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") >makeGeneRegion(start = 25592138, end = 25662215, chromosome = "chr1", strand="+", biomart=mart) V1 1 <html><head> 2 <title>Network Error</title> 3 </head> 4 <body> 5 6 Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id", "ensembl_exon_id", : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list. As it happens, I know that the region corresponds to the gene RHD and the following works as expected. > makeGene(id="RHD", type="hgnc_symbol", biomart=mart) ID:RHD Type:hgnc_symbol Exons in Ensembl: ensembl_gene_id ensembl_transcript_id ensembl_exon_id exon_chrom_start 1 ENSG00000187010 ENST00000328664 ENSE00001463282 25598981 2 ENSG00000187010 ENST00000328664 ENSE00001799547 25611064 3 ENSG00000187010 ENST00000328664 ENSE00001784803 25617132 4 ENSG00000187010 ENST00000328664 ENSE00001626654 25627437 5 ENSG00000187010 ENST00000328664 ENSE00001730743 25628011 exon_chrom_end rank strand biotype 1 25599186 1 1 protein_coding 2 25611250 2 1 protein_coding 3 25617282 3 1 protein_coding 4 25627584 4 1 protein_coding 5 25628177 5 1 protein_coding Can anyone suggest why makeGeneRegion isn't behaving? Regards, Mark > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] diagram_1.5 shape_1.2.2 GenomeGraphs_1.8.0 [4] biomaRt_2.4.0 Rsamtools_1.2.0 Biostrings_2.17.26 [7] GenomicFeatures_1.2.1 GenomicRanges_1.2.1 IRanges_1.8.2 loaded via a namespace (and not attached): [1] Biobase_2.8.0 BSgenome_1.16.5 DBI_0.2-5 RCurl_1.4-3 [5] RSQLite_0.9-2 rtracklayer_1.10.4 tools_2.12.0 XML_3.2-0
biomaRt GenomeGraphs biomaRt GenomeGraphs • 1.2k views
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Mike Smith ★ 6.6k
@mike-smith
Last seen 1 hour ago
EMBL Heidelberg
Hi Mark, The default biomart.org server is extremely slow for me too (although I do eventually get a result rather tha the network error HTML page you appear to be getting). Perhaps try the ensembl server instead: mart <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host = "www.ensembl.org") I get a much quicker response from that server. Using your code I still don't get any exons, but swaping out <chromosome =="" "chr1"=""> and using <chromosome =="" 1=""> seems to do the job nicely. -- Mike Smith PhD Student Computational Biology Group Cambridge University On Tue, Nov 9, 2010 at 10:39 AM, Mark Dunning <mark.dunning@gmail.com>wrote: > Hi all, > > I am trying to use the makeGeneRegion function in GenomeGraphs to get > the locations of exons within a particular genomic region. The > function seems to take an extraordinarily long time and then returns > an error. > > > >mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") > >makeGeneRegion(start = 25592138, end = 25662215, chromosome = "chr1", > strand="+", biomart=mart) > > > > V1 > 1 > <html><head> > 2 Network > Error > 3 > </head> > 4 > <body> > 5 bgcolor="#003399"> > 6 > > Error in getBM(c("ensembl_gene_id", "ensembl_transcript_id", > "ensembl_exon_id", : > The query to the BioMart webservice returned an invalid result: the > number of columns in the result table does not equal the number of > attributes in the query. Please report this to the mailing list. > > > > As it happens, I know that the region corresponds to the gene RHD and > the following works as expected. > > > makeGene(id="RHD", type="hgnc_symbol", biomart=mart) > ID:RHD > Type:hgnc_symbol > Exons in Ensembl: > ensembl_gene_id ensembl_transcript_id ensembl_exon_id exon_chrom_start > 1 ENSG00000187010 ENST00000328664 ENSE00001463282 25598981 > 2 ENSG00000187010 ENST00000328664 ENSE00001799547 25611064 > 3 ENSG00000187010 ENST00000328664 ENSE00001784803 25617132 > 4 ENSG00000187010 ENST00000328664 ENSE00001626654 25627437 > 5 ENSG00000187010 ENST00000328664 ENSE00001730743 25628011 > exon_chrom_end rank strand biotype > 1 25599186 1 1 protein_coding > 2 25611250 2 1 protein_coding > 3 25617282 3 1 protein_coding > 4 25627584 4 1 protein_coding > 5 25628177 5 1 protein_coding > > > Can anyone suggest why makeGeneRegion isn't behaving? > > Regards, > > Mark > > > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] diagram_1.5 shape_1.2.2 GenomeGraphs_1.8.0 > [4] biomaRt_2.4.0 Rsamtools_1.2.0 Biostrings_2.17.26 > [7] GenomicFeatures_1.2.1 GenomicRanges_1.2.1 IRanges_1.8.2 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 BSgenome_1.16.5 DBI_0.2-5 RCurl_1.4-3 > [5] RSQLite_0.9-2 rtracklayer_1.10.4 tools_2.12.0 XML_3.2-0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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