Hi Richard,

The Ensembl BioMart "gene" datasets (hsapiens_gene_ensembl,....) are
transcript/gene centric.  So only annotation related to genes/transcripts
can be retrieved from those datasets.
You can get all cytoband annotation for all genes as follows:

ensembl <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
annotation <- getBM(c('ensembl_gene_id','hgnc_symbol','band'),
filters="with_hgnc",values=TRUE,mart=ensembl)

Note that I am only retrieving genes with an hgnc_symbol in the above
query, if you also want the ones without symbols do:

annotation <- getBM(c('ensembl_gene_id','hgnc_symbol','band'),mart=ensembl)

Cheers,
Steffen


On Wed, May 1, 2013 at 3:13 AM, Richard Birnie [guest] <
guest@bioconductor.org> wrote:

>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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