[BioC] alphabetByCycle not working on AAStringSet

[Martin Morgan]

On 12/17/2013 04:11 AM, Nicolas Delhomme wrote:
> Hej Bioc!
>
> When I want to get the alphabetByCycle for an AAStringSet, I get "Error in alphabetByCycle(aa) : unknown class ‘AAString’".
>

this is enabled in ShortRead 1.21.8, thanks Nico. Martin

> Here is a toy example:
>> aa <- AAStringSet(c("ARN","DCQ"))
>> aa
> A AAStringSet instance of length 2
>      width seq
> [1]     3 ARN
> [2]     3 DCQ
>> alphabetByCycle(aa)
> Error in alphabetByCycle(aa) : unknown class ‘AAString'
>
> My sessionInfo()
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C            LC_COLLATE=C         LC_MONETARY=C        LC_MESSAGES=C
>   [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RColorBrewer_1.0-5   ShortRead_1.20.0     Rsamtools_1.14.2     lattice_0.20-24      GenomicRanges_1.14.0 Biostrings_2.30.0
> [7] XVector_0.2.0        IRanges_1.20.0       BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.22.0      bitops_1.0-6        grid_3.0.2          hwriter_1.3         latticeExtra_0.6-26 stats4_3.0.2
> [7] tools_3.0.2         zlibbioc_1.8.0
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Nathaniel Street Lab
> Department of Plant Physiology
> Umeå Plant Science Center
>
> Tel: +46 90 786 7989
> Email: nicolas.delhomme at plantphys.umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
>
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