Hi Wolfgang,

It is on my todo list and my plan was to add this into the devel version of
biomaRt before the next Bioconductor release so it would be available to
all in the next release.  I can make this available sooner in the devel
version if this feature is highly needed.

Cheers,
Steffen

On Sat, Jun 9, 2012 at 2:08 AM, Wolfgang Huber <whuber@embl.de> wrote:

> Dear Vince
>
> thanks for this post - was this ever resolved / followed up ?
>
>        best wishes
>        Wolfgang
>
> Mar/9/12 11:29 PM, Vince S. Buffalo scripsit::
>
>  Hi bioc-devel,
>>
>> I noticed today that BioMart queries to phytozome return columns out of
>> order. I found mention of this issue here:
>> https://stat.ethz.ch/**pipermail/bioconductor/2011-**October/041384.html<https://stat.ethz.ch/pipermail/bioconductor/2011-October/041384.html>Currently,
>> biomaRt's getBM() makes the assumption that the results are returned in
>> the
>> same order that the attributes are specified when setting column names,
>> which is incorrect.
>>
>> According to the BioMart documentation (version 0.8), the query XML format
>> has an option to set header="1" (see page 63 here:
>> http://www.biomart.org/other/**rc6_documentation.pdf<http://www.biomart.org/other/rc6_documentation.pdf>)
>> which appears to solve
>> this issue. I've changed this locally in R/biomaRt.R's getBM(), removed
>> the
>> colnames(results) = attributes in the second to last line of the function,
>> and it appears to work with phytozome and ensembl. I can't find on the
>> BioMart website whether this is a recent addition to the query format. If
>> it only works with some recent BioMart versions, could we add header="1"
>> to
>> the query for the appropriate versions and then call warning() to warn
>> users their column names may be incorrect for other versions? I would be
>> happy to supply a patch if needed.
>>
>> best,
>> Vince
>>
>>
>
> --
> Best wishes
>        Wolfgang
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/**units/genome_biology/huber<http://www.embl.de/research/units/genome_biology/huber>
>
>
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