[BioC] DNAString: Error for long sequences
Ann Hess
hess at stat.colostate.edu
Tue Aug 26 17:31:43 CEST 2008
I am having trouble creating long (~1000+ characters) DNAStrings.
Specifically, I seem to get an error when R has to go to a new line in the
command window when copy/pasting the sequence from an R script (with no
breaks). I recently upgraded R and BioConductor, but previously I did not have this problem.
Code and error is below. Any suggestions?
Ann
**********************************************************
> library(Biostrings)
# "Short" example with no error
> Temp1<-DNAString(
+ "AACACACGCATCTCACGCCGAGGACCTGGGATCG.....")
> Temp1
969-letter "DNAString" instance
# "Long" example, such that R needs a new line to complete the sequence
> Temp2<-DNAString(
+ "AACACACGCATCTCACGCCGAGGACCTGGGATCG.....
+ TTTTTCGCATAGTGCTCAA")
Error in charToXRaw(x, start = start, end = end, width = width, lkup =
lkup, :
key 10 not in lookup table
> sessionInfo()
R version 2.7.1 (2008-06-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Biostrings_2.8.17
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