[Bioc-devel] biomaRt XML query "header" attribute

Wolfgang Huber whuber at embl.de
Sat Jun 9 11:08:55 CEST 2012

Dear Vince

thanks for this post - was this ever resolved / followed up ?

	best wishes

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 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) 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 Huber

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