[BioC] an erro related with RNAStringSet

[Hervé Pagès]

On 03/16/2012 03:21 PM, wang peter wrote:
> aa<-read.table("")
> x=as.character(aa[,1])
> names(x)=1:length(x)
> writeFasta(RNAStringSet(x, use.names=TRUE),"miRNA")
>
> Error in .Call2("new_XStringSet_from_CHARACTER", classname, elementType,  :
>    key 101 not in lookup table

Looks like you are trying to put non-RNA letters into an RNA object:

   > RNAStringSet("e", use.names=TRUE)
   Error in .Call2("new_XString_from_CHARACTER", classname, x, 
start(solved_SEW),  :
     key 101 not in lookup table

In BioC devel, the error message also displays the letter associated
with the code:

   > RNAStringSet("accgaggaudnugeacc", use.names=TRUE)
   Error in .Call2("new_XString_from_CHARACTER", classname, x, 
start(solved_SEW),  :
     key 101 (char 'e') not in lookup table

H.

>
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
> [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
> [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
> [4] LC_NUMERIC=C
> [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.12.4    latticeExtra_0.6-19 RColorBrewer_1.0-5
> Rsamtools_1.6.3
> [5] lattice_0.20-0      Biostrings_2.22.0   GenomicRanges_1.6.7
> IRanges_1.12.6
> [9] biomaRt_2.10.0
>
> loaded via a namespace (and not attached):
>   [1] Biobase_2.14.0     bitops_1.0-4.1     BSgenome_1.22.0
> grid_2.14.1        hwriter_1.3
>   [6] RCurl_1.91-1.1     rtracklayer_1.14.4 tools_2.14.1
> XML_3.9-4.1        zlibbioc_1.0.0
>
>
>
>
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
Seattle, WA 98109-1024

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