Pete, Thanks for the bug report. This is fixed in IRanges 1.17.11. Note that the data inside the rle must be a factor. Adding levels to an Rle after the fact doesn't create a factor-Rle. x = Rle(c(2,3,1,2,3,2),rep(2,6)) levels(x) = as.character(0:5) This is a numeric-Rle with no levels. > x numeric-Rle of length 12 with 6 runs Lengths: 2 2 2 2 2 2 Values : 2 3 1 2 3 2 > table(x) 1 2 3 2 6 4 The same is true for a numeric vector. table() on a non-factor argument will drop unused levels. v <- rep(c(2,3,1,2,3,2), each=2) levels(v) <- 0:5 > table(v) v 1 2 3 2 6 4 If we create a factor-Rle, table() will retain all levels. x_f = Rle(factor(rep(c(2,3,1,2,3,2), each=2), levels=0:5)) > x_f factor-Rle of length 12 with 6 runs Lengths: 2 2 2 2 2 2 Values : 2 3 1 2 3 2 Levels(6): 0 1 2 3 4 5 > table(x_f) 0 1 2 3 4 5 0 2 6 4 0 0 Valerie On 10/29/2012 08:13 PM, Valerie Obenchain wrote: > Thanks Pete. I'll look into it. > > Valerie > > On 10/29/12 14:28, Peter Haverty wrote: >> Dear Group, >> >> table(Rle) seems to ignore empty levels. >> >> x = Rle(c(2,3,1,2,3,2),rep(2,6)) >> levels(x) = as.character(0:5) >> table(x) >> table(factor(as.numeric(x),levels=as.character(0:5))) >> >> I am using R 2.15.1 and IRanges 1.17.1. >> >> Regards, >> Pete >> >> ____________________ >> Peter M. Haverty, Ph.D. >> Genentech, Inc. >> phaverty at gene.com >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor