I guess you mean dropSeqlevels, not keepSeqlevels? That should work. But
your function needs some tweaking, I think. The function should just take
the seqnameStyle from the object. There's no need to require the user to
specify it, and then check for consistency. I would like to be able to just
call:

keepStandardChromosomes(trans)

Also, I think you made GenomicRanges depend on AnnotationDbi. That's a
major change. Before, it was just in Suggests. Did you discuss this with
anyone?

Michael




On Fri, Dec 27, 2013 at 11:37 AM, Arora, Sonali <sarora@fhcrc.org> wrote:

>  Hi Michael,
>
> We decided to come up with one function called keepStandardChromosomes()
> which
> is a wrapper for both the functions suggested by you (i.e.,
> keepPrimaryChromosomes() and keepAutosomes() )
>
> Here is an example:
>
> library(AnnotationDbi)
> library(GenomicRanges)
> txdb <- loadDb(system.file("extdata", "UCSC_knownGene_sample.sqlite",
>                            package="GenomicFeatures"))
>
> trans <- transcripts(txdb)
> seqlevels(trans)
>
> #gets all GRanges for Human chromosomes : 1-22,X,Y,M
> got <- keepStandardChromosomes(trans,style="UCSC", species="Homo sapiens")
> seqlevels(got)
>
> #for getting only autosomes, one could then extract using keepSeqlevels()
> #as shown earlier:
> keepSeqlevels(got,c("chrX","chrY"))
> keepSeqlevels(got,c("chrX","chrY", "chrM"))
>
> Thanks and Regards
> Sonali.
>
> On 12/25/2013 4:15 AM, Michael Lawrence wrote:
>
> Awesome -- how about keepAutosomes?
>
>
> On Tue, Dec 24, 2013 at 1:11 PM, Arora, Sonali <sarora@fhcrc.org> wrote:
>
>>  Hi everyone,
>>
>> We are pleased to announce that we have added a new function called
>> keepStandardChromosomes() to  GenomicRanges(1.15.18)  - devel branch.
>>
>> This function allows a user to subset a given object (containing a
>> seqinfo class) to
>> retain only the primary chromosomes and the autosomes.
>>
>> Please feel free to get back if you face any issues.
>>
>> Thanks,
>> Sonali Arora.
>>
>> On 12/16/2013 11:01 AM, Michael Lawrence wrote:
>>
>>  Awesome, thanks, Sonali. And welcome to the team.
>>
>>  Michael
>>
>>
>> On Mon, Dec 16, 2013 at 10:38 AM, Arora, Sonali <sarora@fhcrc.org> wrote:
>>
>>> Hi Michael,
>>>
>>> That is an extremely interesting question. We have a couple of ideas and
>>> are beginning to work on it.
>>> We hope to come up with something soon.
>>>
>>> Thanks,
>>> Sonali.
>>>
>>>
>>> On 12/16/2013 6:14 AM, Michael Lawrence wrote:
>>>
>>>>   should be stored with the Seqinfo. It could be imputed
>>>> (along with the isCircular I think) via th
>>>>
>>>
>>>  _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>>
>
>

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