Re: [Bioc-devel] seqlevelsStyle<- doesn't work for GRanges object

[Tengfei Yin]

Thanks a lot, it works!

cheers

Tengfei


On Fri, Apr 11, 2014 at 5:37 AM, Hervé Pagès <hpa...@fhcrc.org> wrote:

> Hi Tengfei,
>
> Should be fixed in GenomicRanges 1.15.45
>
>
> On 04/10/2014 03:29 PM, Tengfei Yin wrote:
>
>> forget to say "thank you" in the end :)
>>
>
> You're welcome :)
>
> H.
>
>
>>
>> On Thu, Apr 10, 2014 at 6:22 PM, Tengfei Yin <tengfei....@sbgenomics.com>
>> wrote:
>>
>>  Hi all,
>>>
>>> "seqlevelsStyle<-" method does work for me in devel-branch, I haven't dig
>>> into it yet, please check out the code below and its output.
>>>
>>> ## for you to paste
>>> library(GenomicRanges)
>>> gr <- GRanges("chr1", IRanges(1, 3))
>>> seqlevelsStyle(gr) ## works
>>> seqlevelsStyle(gr) <- "NCBI" ## fail
>>> seqnameStyle(gr) ## works
>>> seqnameStyle(gr) <- "NCBI" ## works
>>> library(GenomeInfoDb)
>>> seqlevelsStyle(gr) <- "NCBI" ## fail
>>> sessionInfo()
>>>
>>> ## output
>>>
>>>> gr <- GRanges("chr1", IRanges(1, 3))
>>>> seqlevelsStyle(gr) ## works
>>>>
>>> [1] "UCSC"
>>>
>>>> seqlevelsStyle(gr) <- "NCBI" ## fail
>>>>
>>> Error in (function (classes, fdef, mtable)  :
>>>    unable to find an inherited method for function
>>> ‘seqlevelsStyle<-’ for
>>> signature ‘"GRanges"’
>>>
>>>  seqnameStyle(gr) ## works
>>>>
>>> [1] "UCSC"
>>> Warning message:
>>> 'seqnameStyle' is deprecated.  Use 'seqlevelsStyle()' instead.
>>>
>>>> seqnameStyle(gr) <- "NCBI" ## works
>>>> library(GenomeInfoDb)
>>>> seqlevelsStyle(gr) <- "NCBI" ## fail
>>>>
>>> Error in (function (classes, fdef, mtable)  :
>>>    unable to find an inherited method for function
>>> ‘seqlevelsStyle<-’ for
>>> signature ‘"GRanges"’
>>>
>>>  sessionInfo()
>>>>
>>> R Under development (unstable) (2014-01-06 r64681)
>>> Platform: x86_64-apple-darwin13.0.2 (64-bit)
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] GenomicRanges_1.15.44 GenomeInfoDb_0.99.31  IRanges_1.21.45
>>> [4] BiocGenerics_0.9.3
>>>
>>> loaded via a namespace (and not attached):
>>> [1] stats4_3.1.0  XVector_0.3.7
>>>
>>> --
>>> Tengfei Yin, PhD
>>> Seven Bridges Genomics
>>> sbgenomics.com
>>> 625 Mt. Auburn St. Suite #208
>>> Cambridge, MA 02138
>>> (617) 866-0446
>>>
>>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
Tengfei Yin, PhD
Seven Bridges Genomics
sbgenomics.com
625 Mt. Auburn St. Suite #208
Cambridge, MA 02138
(617) 866-0446

        [[alternative HTML version deleted]]


_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel