Hi all, It looks as if the as.vector call to a run length encoded factor turns it to a vector of characters. Did this happen on accident, or was it a deliberate design decision? Previously: R-2.12, IRanges_1.7.19, GenomicRanges_1.1.20 (A factor of length one is returned): R> a <- Rle(strand(c('+', '-', '+', '+', '-'))) R> as.vector(a[1]) [1] + Levels: + - * ============================= Now: R-2.12, IRanges_1.7.31, GenomicRanges_1.1.20 (The factor is converted to a character) R> a <- Rle(strand(c('+', '-', '+', '+', '-'))) R> as.vector(a[1]) [1] "+" It seems like it would do what is expected (by me :-) if the `getMethod('as.vector', c("Rle", "missing"))` was changed from: function (x, mode = "any") rep.int(as.vector(runValue(x)), runLength(x)) To: function (x, mode = "any") rep.int(runValue(x), runLength(x)) but, upon further inspection, it seems like this was how it was defined previously anyway, so ... I guess something motivated this change? The complete sessionInfo for my last (buggy(?)) case is: R version 2.12.0 Under development (unstable) (2010-07-07 r52477) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicRanges_1.1.20 IRanges_1.7.31 loaded via a namespace (and not attached): [1] tools_2.12.0 Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

On 08/31/2010 07:15 AM, Steve Lianoglou wrote: > Hi all, > > It looks as if the as.vector call to a run length encoded factor turns > it to a vector of characters. > > Did this happen on accident, or was it a deliberate design decision? Bug fix > x = factor(letters) > as.vector(x) [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" [20] "t" "u" "v" "w" "x" "y" "z" > as.factor(x) [1] a b c d e f g h i j k l m n o p q r s t u v w x y z Levels: a b c d e f g h i j k l m n o p q r s t u v w x y z So > Rle(factor(letters)) 'factor' Rle of length 26 with 26 runs Lengths: 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Values : a b c d e f g h i j k l m n o p q r s t u v w x y z Levels(26): a b c d e f g h i j k l m n o p q r s t u v w x y z > as.vector(Rle(factor(letters))) [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" [20] "t" "u" "v" "w" "x" "y" "z" > as.factor(Rle(factor(letters))) [1] a b c d e f g h i j k l m n o p q r s t u v w x y z Levels: a b c d e f g h i j k l m n o p q r s t u v w x y z There might be edge cases where our own code has not caught up with the fix; please let us know... > packageDescription('IRanges')$Version [1] "1.7.32" Martin > > Previously: > > R-2.12, IRanges_1.7.19, GenomicRanges_1.1.20 > (A factor of length one is returned): > > R> a <- Rle(strand(c('+', '-', '+', '+', '-'))) > R> as.vector(a[1]) > [1] + > Levels: + - * > > ============================= > > Now: > R-2.12, IRanges_1.7.31, GenomicRanges_1.1.20 (The factor is converted > to a character) > > R> a <- Rle(strand(c('+', '-', '+', '+', '-'))) > R> as.vector(a[1]) > [1] "+" > > It seems like it would do what is expected (by me :-) if the > `getMethod('as.vector', c("Rle", "missing"))` was changed from: > > function (x, mode = "any") > rep.int(as.vector(runValue(x)), runLength(x)) > > To: > > function (x, mode = "any") > rep.int(runValue(x), runLength(x)) > > but, upon further inspection, it seems like this was how it was > defined previously anyway, so ... I guess something motivated this > change? > > The complete sessionInfo for my last (buggy(?)) case is: > > R version 2.12.0 Under development (unstable) (2010-07-07 r52477) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C > [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C > LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicRanges_1.1.20 IRanges_1.7.31 > > loaded via a namespace (and not attached): > [1] tools_2.12.0 > > Thanks, > -steve > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793