[Bioc-devel] biomaRt::getBM column names

Hi Martin,

The original behaviour is offered through bmHeader = FALSE in the getBM query.
Below is the long story why this change came about (it would be good to hear
which solution is preferred by others):

In most cases getBM returns the result in the order of the attributes in the
input query.  So what getBM used to do is make the attributes vector the column
names of the query result.  This return order is however not preserved in
instances where one does a query over multiple datasets e.g. mouse and human.
  In that case one can not predict the order of the result and this would make
the column names not match the actually returned fields.  So there was a push
that getBM uses the header information provided by the BioMart service which is
available upon request.  This ensures that the column names are always correct.
  The downside though is that the column names returned by the BioMart service
are not the attribute name but it's description so instead of a column name
'affy_hg_u95av2'  we get 'Affy HG U95AV2 probeset'.  To keep the column naming
as it used to be, I then would map the attribute description back to the
attribute name and then use the corresponding attribute name as column name for
the query result.  This worked until I discovered that the attribute
descriptions are not unique, so there is no one to one mapping from a
description to a attribute name and this made the getBM code crash.  I then
decided that the best thing to do is by default to use the headers provided by
the BioMart service to ensure queries never crash due to problems on the R side.
  And to enable attribute naming as it originally was done I added the
bmHeader=FALSE option.  This will be correct in most uses except for queries
across multple datasets.

Best,
Steffen



On Fri, Jun 7, 2013 at 5:31 PM, Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>> wrote:

    Hi Steffen --

    getBM now returns the 'description' rather than 'name' of biomaRt columns, e.g.,

          mart <- useMart("ensembl")
          datasets <- listDatasets(mart)
          mart<-useDataset("hsapiens___gene_ensembl",mart)
          df <- getBM(attributes=c("affy_hg___u95av2", "hgnc_symbol",
                                   "chromosome_name" , "band"),

    filters="affy_hg_u95av2",__values=c("1939_at","1503_at","__1454_at"),,
                 mart=mart)

    returns

     > df ## devel

       Affy HG U95AV2 probeset HGNC symbol Chromosome Name   Band
    1                 1939_at        TP53              17  p13.1
    2                 1503_at       BRCA2              13  q13.1
    3                 1454_at       SMAD3              15 q22.33

    rather than

     > df  ## release

       affy_hg_u95av2 hgnc_symbol chromosome_name   band
    1        1939_at        TP53              17  p13.1
    2        1503_at       BRCA2              13  q13.1
    3        1454_at       SMAD3              15 q22.33

    This makes it difficult to access columns via df$... (breaking code in at
    least a couple of packages) and it is a little confusing to ask for
    'affy_hg_u95av2' but get 'Affy HG U95AV2 probeset'. I wonder if the original
    behaviour could be offered, either as an option or as a similarly named
    function, or (my preference) the new behavior could be provided by something
    like getBiomart() -- fancy function name for fancy column names?

    Martin
    --
    Computational Biology / Fred Hutchinson Cancer Research Center
    1100 Fairview Ave. N.
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    Location: Arnold Building M1 B861
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