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
>>
>>
>> _______________________________________________
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>> mailing list
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>>
>>
>
>
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