[BioC] BSgenome.Mmulatta.UCSC
Martin Morgan
mtmorgan at fhcrc.org
Thu Nov 28 17:52:25 CET 2013
On 11/28/2013 07:20 AM, Brian Smith wrote:
> Hi Martin,
>
> Thanks for the reply!
>
> I get the following:
>
> --------------------------------------------------
> > library(AnnotationHub)
> > hub = AnnotationHub()
> > Mmulatta2 =
> hub$ensembl.release.73.fasta.macaca_mulatta.dna.Macaca_mulatta.MMUL_1.73.dna.toplevel.fa.rz
> Warning message:
> In .getResource(x, name) : incomplete path
probably you are using a version of R for which this resource is not available.
There is tab completion, and once you get to
hub$ensembl.release.7
press the tab key. Likely you'll see
> hub$ensembl.release.7
hub$ensembl.release.70. ... [427] hub$ensembl.release.72. ... [393]
hub$ensembl.release.71. ... [426]
and you can complete to
Mmullata2 =
hub$ensembl.release.72.fasta.macaca_mulatta.dna.Macaca_mulatta.MMUL_1.72.dna.toplevel.fa.rz
Print Mmullata2 to the console to ensure that it is an 'FaFile' object.
> > getSeq(Mmulatta2, GRanges("1", IRanges(567089, width=1))) #A DNAStringSet
> instance of length 1
> Error in (function (classes, fdef, mtable) :
> unable to find an inherited method for function ‘getSeq’ for signature
> ‘"character"’
>
> --------------------------------------------------
>
> Am I doing something wrong, or do I need to install another package?
>
> thanks!
>
>
> On Wed, Nov 27, 2013 at 2:33 PM, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
> On 11/27/2013 08:58 AM, Brian Smith wrote:
>
> Hi,
>
> I wanted to use the Mmulatta genome in bioconductor, but using
> "available.genomes()", I see that only the rheMac2 (from 2006) is
> available.
>
> UCSC also shows rheMac3 (from 2010). Is there a way that I can
> download/incorporate this?
>
> Essentially, I want to find the nucleotide at specific positions in the
> rhesus genome (e.g. chr1 - 567089).
>
>
> Depending on what you're actually interested in,
>
> library(AnnotationHub)
> hub = AnnotationHub()
> Mmulatta =
> hub$ensembl.release.73.fasta.__macaca_mulatta.dna.Macaca___mulatta.MMUL_1.73.dna.__toplevel.fa.rz
>
> and then
>
> > getSeq(Mmulatta, GRanges("1", IRanges(567089, width=1))) A DNAStringSet
> instance of length 1
> width seq names
> [1] 1 G 1
>
> Martin
>
>
> thanks!!
>
> [[alternative HTML version deleted]]
>
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--
Computational Biology / Fred Hutchinson Cancer Research Center
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PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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