Yeah I just realized that when I pasted it in to execute it.  Trying to
find where exactly I did this in the past (because it worked back then)



On Thu, Mar 15, 2012 at 10:42 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Howdy,
>
> On Thu, Mar 15, 2012 at 1:10 PM, Tim Triche, Jr. <tim.triche@gmail.com>
> wrote:
> > what you want to do is create a Ranges object and then get a View of the
> > sequences.
> >
> >
> > library(Biostrings)
> > library(GenomicRanges)
> > mirs <- GRanges( paste('chr', mirInfo[i,1], sep=''),
> >                 IRanges(start=mirInfo[i,4], width=1),
> >                 strand=whereverYouKeepTheStrand )
> > upstream <- flank(mirs, 200)
> > upseqs <- Views(Rnorvegicus, mirs)
> > show(upseqs)
> >
> > Untested because I am lazy as hell, but it should work, and be a LOT
> faster.
>
> Maybe in R 2.16 ...
>
> R> Views(Hsapiens, GRanges(c('chr1', 'chr2'), IRanges(c(6e6, 6e6),
> width=10), '+'))
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "Views", for
> signature "BSgenome"
>
> ;-)
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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