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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