Thanks, Herve!
To answer Tim's question (though it has become irrelevant after Herve's
solution): because I'd rather not add VariantAnnotation to my dependency
tree for only a couple of lines of code. It also seemed like the sort
of thing that should be possible with a DNAStringSetList constructor, so
I'm glad it will be starting tomorrow.
Stephanie
On 4/19/13 12:35 PM, Hervé Pagès wrote:
Hi Stephanie,
On 04/19/2013 11:55 AM, Stephanie M. Gogarten wrote:
Hi all,
There is a non-exported function in VariantAnnotation called
.toDNAStringSetList that converts a vector of comma-separated character
strings to a DNAStringSetList. I'd like to use this code in a package
I'm working on. Would it make sense to export this from Biostrings? If
not, what is the proper way to attribute code if I borrow a few lines
from .toDNAStringSetList?
This should be a 1-liner but the 1-liner fails at the moment because the
DNAStringSetList() constructor doesn't work on a list:
> comma_sep_strings <- c("AA,TT", "ACGT", "", "TT,A,,TAG")
> DNAStringSetList(strsplit(comma_sep_strings, ",", fixed=TRUE))
Error in strsplit(comma_sep_strings, ",") : non-character argument
Of course this should work (and it will work tomorrow after you run
biocLite()). In the mean time the workaround is to use do.call():
> do.call(DNAStringSetList, strsplit(comma_sep_strings, ",",
fixed=TRUE))
DNAStringSetList of length 4
[[1]] AA TT
[[2]] ACGT
[[3]] A DNAStringSet instance of length 0
[[4]] TT A TAG
Cheers,
H.
PS: Calling strsplit() with 'fixed=TRUE' makes it about 4x faster :-)
thanks,
Stephanie
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