[Bioc-devel] converting character vector to DNAStringSetList
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, Herv? Pag?s 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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