[BioC] unusual behavior when concatenating DNAStringSets

[Martin Morgan]

On 09/24/2010 05:51 AM, Andrew Yee wrote:
> Hi, I've posted the same question to the bio-sig-sequencing list (
> https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2010-September/001564.html)
> two days ago, but also interested to see if the main Bioconductor group has
> any input as follows:
> 
> I encountered some unusual behavior when concatenating multiple
> DNAStringSet objects as follows:
> 
> library('Biostrings')
> 
> x <- DNAStringSet('ATA')
> y <- DNAStringSet('GCG')
> z <- DNAStringSet('AGA')
> 
> foo <- rep(list(x,y,z),1) # I was exploring to see if the length of the list
> made a difference (it doesn't)
> do.call(c, foo) # creates a DNAStringSet
> 
> names(foo) <- c('x', 'y', 'z')
> do.call(c, foo) # creates a DNAStringSet
> 
> names(foo) <- c('a', 'b', 'c')
> do.call(c, foo) # creates a list instead, not a DNAStringSet

Hi Andrew -- I have partially answered your original post.

Martin

> 
> It seems that in the last case, a list is created rather than a
> DNAStringSet.  It seems that the operation in sensitive to the names()
> of the list.  Or is there an alternative means of concatenating
> multiple DNAStringSets?
> 
> Thanks,
> Andrew
> 
> 
>> sessionInfo()
> R version 2.11.1 Patched (2010-09-04 r52880)
> 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=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       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_2.16.9 IRanges_1.6.17
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0
> 
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> 
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