Hi Julian,
On 04/04/2013 03:50 AM, Julian Gehring wrote:
Hi,
Unlisting does not work on a list with a 'DNAString' as a element, the
resulting object is still a list. Is this behavior intentional? Here
an example that reproduces the issue in both the latest
R-devel/bioc-devel and R-2.15.3/bioc-stable.
library(Biostrings)
d = DNAString("TTGAAAA-CTC-N")
class(d) ## -> DNAString
l = list(d)
class(l) ## -> list
u = unlist(l)
class(u) ## -> still a list, should be the same as 'd'
You're putting an S4 object inside an ordinary list so when you
call unlist() on that list, you are actually calling base::unlist(),
which doesn't know how to handle list elements that are S4 objects.
Maybe it should. Conceptually, non-recursive unlisting is equivalent
to 'do.call(c, l)' so it would be expected to work as long as trying
to combine the individual list elements with c() works.
Maybe base::unlist() could be improved to handle this situation but
that means someone has enough motivation to bring this on the
R-devel mailing list.
In the meantime you can unlist you're ordinary list with:
> do.call(c, l)
13-letter "DNAString" instance
seq: TTGAAAA-CTC-N
Or, even better, use a DNAStringSet object to store a list of DNAString
objects. That's exactly what a DNAStringSet object is:
> dna <- DNAStringSet(c("TTGAAAA-CTC-N", "", "ATTG"))
> dna
A DNAStringSet instance of length 3
width seq
[1] 13 TTGAAAA-CTC-N
[2] 0
[3] 4 ATTG
> is(dna, "List")
[1] TRUE
> elementType(dna)
[1] "DNAString"
> dna[[1]]
13-letter "DNAString" instance
seq: TTGAAAA-CTC-N
> unlist(dna)
17-letter "DNAString" instance
seq: TTGAAAA-CTC-NATTG
Using a DNAStringSet should generally be much more efficient than
using an ordinary list, not only for unlisting, but for many other
operations.
HTH,
H.
Best wishes
Julian
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Hervé Pagès
Program in Computational Biology
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