[Bioc-devel] biomaRt::getBM column names

Martin Morgan mtmorgan at fhcrc.org
Sat Jun 8 02:31:18 CEST 2013


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.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



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