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

[Hervé Pagès]

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.yin at 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
>>
>
>
>
>
>
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-- 
Hervé Pagès

Program in Computational Biology
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