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Can someone please advise me on an efficient way to deal with
translating coding sequence that contains ambiguities using
Biostrings? The Biostrings translate() function returns an error and
I've not been able to find an obvious work-around.
I did find this exact question posted in March:
https://stat.ethz.ch/pipermail/bioconductor/2011-March/038473.html
And while I think the suggestion of translating to 'X' is a
satisfactory solution, there doesn't seem to have been any further
action or advice offered on this front.
Thank you , Jamie
> translate(DNAString("ATGGGGGCCTGTACC"))
5-letter "AAString" instance
seq: MGACT
> translate(DNAString("ATGGGGGCCTGTACN"))
Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup,
skipcode, :
not a base at pos 15
-- output of sessionInfo():
> sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: i386-apple-darwin9.8.0/i386 (32-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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.22.0 IRanges_1.12.1
loaded via a namespace (and not attached):
[1] tools_2.14.0
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