[BioC] biomaRt not returning expected results

[Richard Birnie [guest]]

Dear Bioconductor users,

I am trying to annotate a series of genomic regions using the biomaRt package. The intention is to retrieve the gene(s) and associated cytoband(s) in these regions. This is working fine for most cases but for one region I am unable to retrieve any annotation.

The specific case is as follows

ensembl <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
annotation <- getBM(attributes=c('hgnc_symbol', 'band'), filters=c('chromosome_name', 'start', 'end'),
                 values=list(2, 2414662, 2457350), mart=ensembl)

These coordinates represent a region on chromosome 2 in cytoband 2p25.3. There are no genes in this region so I would expect this to return just the cytoband (p25.3). What I actually get back is an empty data frame. Even if I search for just the band I still get nothing. I reconstructed the same query through the biomart web interface and got the same (lack of) results.

For a given region of the genome I would expect to get back at least cytoband information at minimum and I don't understand why that isn't happening here. 

All suggestions welcome.
Richard

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 GenomicFeatures_1.10.2                  org.Hs.eg.db_2.8.0                      RSQLite_0.11.2                         
 [5] DBI_0.2-5                               AnnotationDbi_1.20.7                    Biobase_2.18.0                          gdata_2.12.0                           
 [9] reshape_0.8.4                           plyr_1.8                                vcd_1.2-13                              colorspace_1.2-1                       
[13] MASS_7.3-23                             stringr_0.6.2                           reshape2_1.2.2                          biomaRt_2.14.0                         
[17] biovizBase_1.6.2                        ggbio_1.6.6                             gridExtra_0.9.1                         scales_0.2.3                           
[21] ggplot2_0.9.3.1                         GenomicRanges_1.10.7                    IRanges_1.16.6                          BiocGenerics_0.4.0                     
[25] markdown_0.5.4                          knitr_1.1                              

loaded via a namespace (and not attached):
 [1] Biostrings_2.26.3        bitops_1.0-5             BSgenome_1.26.1          cluster_1.14.3           codetools_0.2-8          dichromat_2.0-0          digest_0.6.3            
 [8] evaluate_0.4.3           formatR_0.7              gtable_0.1.2             gtools_2.7.1             Hmisc_3.10-1             labeling_0.1             lattice_0.20-14         
[15] munsell_0.4              parallel_2.15.2          proto_0.3-10             RColorBrewer_1.0-5       RCurl_1.95-4.1           Rsamtools_1.10.2         rtracklayer_1.18.2      
[22] stats4_2.15.2            tools_2.15.2             VariantAnnotation_1.4.12 XML_3.96-0.2             zlibbioc_1.4.0  

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