[BioC] Error when splitting an AAStringSet

Valerie Obenchain vobencha at fhcrc.org
Fri Jan 25 22:23:37 CET 2013


Hi Nico,

We don't currently have an AAStringSetList. The DNAStringSetList is the 
only XStringSetList object we have.

Is this something you would find very useful, i.e., want to request as a 
new feature?

Valerie

On 01/25/2013 03:09 AM, Nicolas Delhomme wrote:
> Hi BioC!
>
> I've got the following error message when I try to split an AAStringSet:
>
> pep<- readAAStringSet("somefile.pep")
>
> labs<- read.delim("someLabel.txt",stringsAsFactors=FALSE,header=FALSE)
>
> peplist<- split(pep,labs[,3])
> Error in relist(x, f) :
>    don't know how to split or relist a AAStringSet object as a AAAStringSetList object
>
> Here are my sessionInfo. I'm not using the latest R version, but one still compatible with Bioc 2.11, so I don't think it's causing the issue.
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Biostrings_2.26.2  IRanges_1.16.4     BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] parallel_2.15.1 stats4_2.15.1
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
>
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