Michael,

Since there is no universal seqnameStyle defined for various objects and 
they do not internally store the seqnameStyle and  species information, 
we decided to ask the user for all 3 arguments. Marc is aware of these 
issues and my code.

Regarding the dependency of GenomicRanges on AnnotationDbi - Martin was 
also concerned about this. Both he and Herve are away at the moment - we 
plan to address this dependency
once they get back.

Thanks and Regards,
Sonali.


On 12/27/2013 12:11 PM, Michael Lawrence wrote:
> 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 <sar...@fhcrc.org 
> <mailto:sar...@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 <sar...@fhcrc.org
>>     <mailto:sar...@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
>>>         <sar...@fhcrc.org <mailto:sar...@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
>>>             <mailto:Bioc-devel@r-project.org> mailing list
>>>             https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
>>
>
>


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