[BioC] Error in makeGeneRegion from GenomeGraphs

Tue Nov 9 11:39:11 CET 2010

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