[BioC] Biomart server down?

[Steffen Durinck]

Hi Fabrice,

You can put this into a biomaRt query as follows for example:

>mart = useMart('functional_genomics', dataset='hsapiens_feature_set')
>feat = getBM(c('fs_display_label_1048','feature_type_description_1048','seq_region_start_1048','seq_region_end_1048'),filters='chromosome_name',values='22',mart=mart)
> head(feat)
        fs_display_label_1048 feature_type_description_1048
1
2 DNase1 - CD4 Enriched Sites    DNase1 Hypersensitive Site
3 DNase1 - CD4 Enriched Sites    DNase1 Hypersensitive Site
4 DNase1 - CD4 Enriched Sites    DNase1 Hypersensitive Site
5 DNase1 - CD4 Enriched Sites    DNase1 Hypersensitive Site
6 DNase1 - CD4 Enriched Sites    DNase1 Hypersensitive Site
  seq_region_start_1048 seq_region_end_1048
1                    NA                  NA
2              51221960            51222408
3              51195540            51195777
4              51175647            51175790
5              51173065            51173230
6              51171513            51171699


Steffen

On Fri, May 20, 2011 at 9:04 AM, Fabrice Tourre <fabrice.ciup at gmail.com> wrote:
> Rhoda,
> Not works for me.
> I used  feature type -> RegulatoryFeature. The xml file is fellow. I
> cannot download anything form the web sites.
>
> Filters Feature Type :
>    RegulatoryFeature
> Attributes:
>    Feature Set
>    Feature Type
>    Chromosome Name
>    Start (bp)
>    End (bp)
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE Query>
> <Query  virtualSchemaName = "default" formatter = "TSV" header = "0"
> uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
>
>        <Dataset name = "hsapiens_feature_set" interface = "default" >
>                <Filter name = "regulatory_feature_type_name" value = "RegulatoryFeature"/>
>                <Attribute name = "fs_display_label_1048" />
>                <Attribute name = "feature_type_name_1048" />
>                <Attribute name = "seq_region_name_1048" />
>                <Attribute name = "seq_region_start_1048" />
>                <Attribute name = "seq_region_end_1048" />
>                <Attribute name = "cell_type_name_1048" />
>        </Dataset>
> </Query>
>
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