[Bioc-devel] converting character vector to DNAStringSetList
Hervé Pagès
hpages at fhcrc.org
Fri Apr 19 21:35:56 CEST 2013
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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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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