[BioC] GetSeq function problems

Droit Arnaud Arnaud.Droit at ircm.qc.ca
Tue Aug 4 18:21:34 CEST 2009


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.

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



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