Entering edit mode
Hi Nico,
Sorry it's taken awhile to get back to you. I wanted to ask about what
behavior you'd expect from a call to unique() on a DNAStringSet, i.e.,
what is your use case?
unique() on a named character vector drops names:
chr <- c(a="A", c="C", aa="A", c="CC")
> unique(chr)
[1] "A" "C" "CC"
Same for a named list:
lst <- list(a="A", c="C", aa="A", c="CC")
> unique(lst)
[[1]]
[1] "A"
[[2]]
[1] "C"
[[3]]
[1] "CC"
unique() on a DNAStringSet was patterned after this behavior. If names
were kept, would it be useful to retain only the name of the first
duplicate? In the data above there are two "A"'s. Would you want 'a'
kept and 'aa' dropped?
Valerie
On 07/26/2012 08:36 AM, Nicolas Delhomme wrote:
> Hi,
>
> I've just realized that a call to unique on a DNAStringSet would
result in the names slot to disappear. There's nothing about this in
the documentation, but if that's the desired effect, warning about it
would be good :-)
>
> Here is how to reproduce it:
>
> library(Biostrings)
> dset<-DNAStringSet(c("A","C"))
> names(dset)<- c("a","a")
> dset
> unique(dset)
>
>
> It gives:
>
>> dset
> A DNAStringSet instance of length 2
> width seq names
> [1] 1 A a
> [2] 1 C a
>> unique(dset)
> A DNAStringSet instance of length 2
> width seq
> [1] 1 A
> [2] 1 C
>
> My sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] Biostrings_2.25.8 IRanges_1.15.24 BiocGenerics_0.3.0
>
> loaded via a namespace (and not attached):
> [1] stats4_2.15.1 tools_2.15.1
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Nathaniel Street Lab
> Department of Plant Physiology
> Ume? Plant Science Center
>
> Tel: +46 90 786 7989
> Email: nicolas.delhomme at plantphys.umu.se
> SLU - Ume? universitet
> Ume? S-901 87 Sweden
>
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