A little further sleuthing suggests that perhaps the more general issues is that > Rle()[FALSE] Error in Rle()[FALSE] : subscript out of bounds # but > vector()[FALSE][NA] [1] NA >-----Original Message----- >From: Cook, Malcolm >Sent: Wednesday, September 04, 2013 9:28 AM >To: 'bioconductor at r-project.org'; 'Hervé Pagès'; 'lawrence.michael at gene.com' >Cc: Chen, Guangbo; Johnston, Jeffrey >Subject: BUG: median(IRanges::Rle(NA),na.rm=TRUE)) should return NA > >Hi, > >I think the Rle functions should preserve semantics from stats. > >Here is at least one case where they do not: > >> median(Rle(NA),na.rm=TRUE) >Error in x[FALSE] : subscript out of bounds > ># but: > >> median(c(NA),na.rm=TRUE) >[1] NA > ># some other border cases: > >> median(c()) >NULL ># arguably correct, if you read the docs and appreciate that as(NA,class(c())) is NULL > >> median(Rle()) >Error in x[FALSE] : subscript out of bounds ># should probably be NULL > > >Agreed? > >Can be fixed? > >Thanks! > >~ Malcolm Cook >Computational Biology / Shilatifard Lab - Stowers Institute for Medical Research - Kansas City >

Hi Malcolm, Thanks for reporting this. A fix is on its way (in IRanges 1.19.30, will be in devel). With this version: > Rle()[FALSE] logical-Rle of length 0 with 0 runs Lengths: Values : More generally, most Vector derivatives now support subsetting by a logical vector longer than 'x' as long as all the out of bounds subscript elements are FALSE: > IRanges(1:2, 4)[c(FALSE, TRUE, FALSE)] IRanges of length 1 start end width [1] 2 4 3 With this change: > median(Rle(NA), na.rm=TRUE) [1] NA and: > median(Rle(integer(0))) [1] NA # NA_integer_ > median(Rle(logical(0))) [1] NA # logical NA > median(Rle()) [1] NA # logical NA The reason the last one returns a logical NA is because the 'Rle()' call is equivalent to 'Rle(logical(0))'. Cheers, H. On 09/04/2013 07:53 AM, Cook, Malcolm wrote: > A little further sleuthing suggests that perhaps the more general issues is that > >> Rle()[FALSE] > Error in Rle()[FALSE] : subscript out of bounds > # but >> vector()[FALSE][NA] > [1] NA > > > > >-----Original Message----- > >From: Cook, Malcolm > >Sent: Wednesday, September 04, 2013 9:28 AM > >To: 'bioconductor at r-project.org'; 'Hervé Pagès'; 'lawrence.michael at gene.com' > >Cc: Chen, Guangbo; Johnston, Jeffrey > >Subject: BUG: median(IRanges::Rle(NA),na.rm=TRUE)) should return NA > > > >Hi, > > > >I think the Rle functions should preserve semantics from stats. > > > >Here is at least one case where they do not: > > > >> median(Rle(NA),na.rm=TRUE) > >Error in x[FALSE] : subscript out of bounds > > > ># but: > > > >> median(c(NA),na.rm=TRUE) > >[1] NA > > > ># some other border cases: > > > >> median(c()) > >NULL > ># arguably correct, if you read the docs and appreciate that as(NA,class(c())) is NULL > > > >> median(Rle()) > >Error in x[FALSE] : subscript out of bounds > ># should probably be NULL > > > > > >Agreed? > > > >Can be fixed? > > > >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 at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319