I've hit this many times and would appreciate support for NA indices. Michael On Mon, Mar 10, 2014 at 1:12 PM, Hervé Pagès <hpages@fhcrc.org> wrote: > Hi Malcolm, > > On one hand, Rle is a Vector subclass and subsetting an Rle is > consistent with subsetting any other Vector subclass (like IRanges, > GRanges, DNAStringSet, etc...) where trying to extract an element > that doesn't exist raises an error. Of course, this is the only > choice for those Vector derivative (that are not Rle's) because > they don't support NAs. > > On the other hand, Rle is a memory efficient replacement for ordinary > atomic vectors, and, ideally, they should be substitutable (which > means the former should mimic the latter as close as possible). > > A choice had to be made 5 years ago when Rle's were implemented > in the IRanges package. Should we revisit that choice and support > subsetting of an Rle by an out-of-bound subscript? Should we also > support NAs in the subscript? > > Thanks, > H. > > > > On 03/10/2014 11:52 AM, Cook, Malcolm wrote: > >> I think the semantics of indexing into an Rles should be the same as >> indexing into the corresponding vector. >> >> But it is not in the case when indices are out of bounds. >> >> Example: >> >> library(IRanges) >> >>> c(1:10)[10:13] >>> >> [1] 10 NA NA NA >> >> Rle(c(1:10))[10:13] >>> >> Error in normalizeSingleBracketSubscript(i, x) : >> subscript contains NAs or out of bounds indices >> >> >> I've made similar arguments before which were taken up, as in >> https://stat.ethz.ch/pipermail/bioconductor/2013-September/054820.html >> >> Is there a good reason NOT to change these semantics? >> >> In the meantime, any suggested clever workarounds to get such extraction >> semantics? >> >> Thanks! >> >> ~ Malcolm Cook >> Computational Biology / Shilatifard Lab - Stowers Institute for Medical >> Research - Kansas City >> >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]