Thanks Steffen,

That's the answer I was looking for before I put some serious work into
something that is probably an ad hoc thing at best.

Tony

On Mon, Nov 23, 2009 at 10:27 AM, <Steffen@stat.berkeley.edu> wrote:

> Hi Tony,
>
> I want to add that in the past we used to return what was used as input to
> the query (filter) also as an attribute.  However this is not
> generalizable as for some attributes/filters the name is different e.g.
> "start_position" in attribute list and "start" in filter list.  And
> sometimes a filter is not present as an attribute. To make our code more
> stable we took this out, and if a user wants such functionality then I
> agree with Wolfgang and it should be a wrapper around getBM that does
> this.
>
> Cheers,
> Steffen
>
>
> > Hi Tony
> >
> > thanks for these good ideas. Both of these you could implement in a
> > small wrapper function around getBM. Once you find that this is a
> > stable, generally useful function, we'd be happy to accept your patch
> > for the biomaRt package!
> >
> > Btw, ENSP00000045065 is a valid protein sequence ID with many hits for
> > it in Google, and indeed in the search box at http://www.ebi.ac.uk. The
> > fact that the hsapiens_gene_ensembl mart does not know a mapping of it
> > to an extant gene name could have all sorts of reasons, historical or
> > scientific, which you could explore at the EBI website.
> >
> >       Best wishes
> >       Wolfgang
> >
> >
> >   Chiang wrote:
> >> Hi Steffen, Sean, Wolfgang,
> >>
> >> I have a question about the return value of the getBM() function. It is
> >> a
> >> data frame object, and in the examples that I have seen, usually if I
> >> want
> >> to map from EMBL IDs to Entrez Gene IDs, we would still also want to map
> >> the
> >> EMBL IDs back to the EMBL IDs so we know what has mapped to what.
> >> Example
> >> code to follow if my explanation is not clear:
> >>
> >> ################
> >> library(biomaRt)
> >> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> >> filters = listFilters(ensembl)
> >> attributes = listAttributes(ensembl)
> >> ##Here are my IDs from String
> >> test = c("9606.ENSP00000045065", "9606.ENSP00000158762",
> >> "9606.ENSP00000174653",
> >> "9606.ENSP00000202967", "9606.ENSP00000204517", "9606.ENSP00000212015",
> >> "9606.ENSP00000220616", "9606.ENSP00000222008", "9606.ENSP00000222390",
> >> "9606.ENSP00000223051")
> >> emblID = sapply(strsplit(test, "\\."), function(x) x[2])
> >> ##And the code I am using for the mapping is:
> >> getBM(attributes=c("ensembl_peptide_id", "entrezgene","ensembl_gene_id",
> >> "hgnc_automatic_gene_name"), filters="ensembl_peptide_id",
> >> values=emblID,
> >> mart=ensembl)
> >> ##################
> >>
> >> So I guess I have two questions: would it be a good idea to always
> >> return
> >> what we input in the output data frame so we would have not to have the
> >> redundant attribute ("ensembl_peptide_id" in my example). Also, if you
> >> ran
> >> the code, you will see that ENSP00000045065 did not map at all , so I
> >> assume
> >> that it is not a valid ensembl_peptide_id (this is a bit strange since I
> >> am
> >> using EMBL IDs); I also want to ask if there is some way to make that
> >> more
> >> transparent...maybe a row of NA values? I realize that these are not
> >> terrible things to work around, but would it not make sense to have
> >> this? If
> >> not, please let me know.
> >>
> >> Cheers,
> >> --Tony
> >>
> >>> sessionInfo()
> >> R version 2.10.0 Patched (2009-10-27 r50222)
> >> x86_64-apple-darwin9.8.0
> >>
> >> locale:
> >> [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> other attached packages:
> >> [1] biomaRt_2.2.0
> >>
> >> loaded via a namespace (and not attached):
> >> [1] RCurl_1.2-1 XML_2.6-0
> >>
> >>      [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > --
> >
> > Best wishes
> >       Wolfgang
> >
> >
> > --
> > Wolfgang Huber
> > EMBL
> > http://www.embl.de/research/units/genome_biology/huber/contact
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>

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