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

[Tengfei Yin]

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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