Entering edit mode
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)
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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
