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
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--
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
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Fax: (206) 667-1319
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