Hi Arnaud,
Droit Arnaud wrote:
> Hello,
>
> I am using getSeq function from Bsgenome to extract a set of sequence.
> When I try the example in the RD file :
>
> library(BSgenome.Celegans.UCSC.ce2)
> myseqs <- data.frame(
> chr=c("chrI", "chrX", "chrM", "chrM", "chrX", "chrI", "chrM", "chrI"),
> start=c(NA, -40, 8510, 301, 30001, 9220500, -2804, -30),
> end=c(50, NA, 8522, 324, 30011, 9220555, -2801, -11),
> strand=c("+", "-", "+", "+", "-", "-", "+", "-")
> )
> getSeq(Celegans, myseqs$chr,
> start=myseqs$start, end=myseqs$end)
>
> a following message appear :
>
> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
> object '.normargSEW' not found
>
> I am wondering if anyone knows this problems.
Please update your installation as explained here:
http://bioconductor.org/docs/install/
and try again. Let us know if the problem persists.
Thanks,
H.
>
> Thanks
>
> Arnaud.
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin9.6.0
>
> locale:
> en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BSgenome.Celegans.UCSC.ce2_1.3.13 BSgenome.Hsapiens.UCSC.hg18_1.3.11
> [3] BSgenome_1.12.2 Biostrings_2.12.1
> [5] GADEM_1.0.0 IRanges_1.2.0
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.4.0 tools_2.9.0
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319