Thanks for taking care of that, Michael. -steve On Sat, Oct 23, 2010 at 11:01 PM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > These issues should now be resolved as of 1.9.1. Sure there's a lot more out > there. > > Michael > > On Fri, Oct 15, 2010 at 6:57 AM, Michael Lawrence <michafla at="" gene.com=""> wrote: >> >> I believe the convention up till now has been to quietly drop the >> metadata, and that makes sense to me. >> >> I can work on fixing some of these methods. I'm sure there are such issues >> all over IRanges, as element metadata was incorporated fairly late in the >> game. >> >> Michael >> >> On Thu, Oct 14, 2010 at 7:43 PM, Steve Lianoglou >> <mailinglist.honeypot at="" gmail.com=""> wrote: >>> >>> Actually, I have a vague feeling of this maybe coming up before (maybe >>> even from me(?)). >>> >>> I understand that it's not clear what to do with the DataFrame >>> values() when merging/intersecting/union/etc. two IRanges, so I would >>> imagine either: >>> >>> (i) dropping the values() from both might be fine (w/ a warning()?); >>> or if you really think this should be an error no matter what >>> >>> (ii) at least give a better error message in this situation so the >>> user can smoke out what's wrong and fix. >>> >>> Thanks, >>> -steve >>> >>> >>> On Thu, Oct 14, 2010 at 9:55 PM, Steve Lianoglou >>> <mailinglist.honeypot at="" gmail.com=""> wrote: >>> > Hi, >>> > >>> > Subject says it all. Here's an example: >>> > >>> > R> library(IRanges) >>> > R> i1 <- IRanges(1, 10) >>> > R> i2 <- IRanges(c(1, 15), width=5) >>> > R> i3 <- i2 >>> > R> values(i3) <- DataFrame(score=1:2) >>> > >>> > R> union(i1, i2) >>> > IRanges of length 2 >>> > ? ?start end width >>> > [1] ? ? 1 ?10 ? ?10 >>> > [2] ? ?15 ?19 ? ? 5 >>> > >>> > R> union(i1, i3) >>> > Error in reduce(c(x0, y), drop.empty.ranges = TRUE) : >>> > ?error in evaluating the argument 'x' in selecting a method for >>> > function 'reduce' >>> > >>> > R> setdiff(i1, i2) >>> > IRanges of length 1 >>> > ? ?start end width >>> > [1] ? ? 6 ?10 ? ? 5 >>> > >>> > R> setdiff(i1, i3) >>> > Error in gaps(union(gaps(x, start = start, end = end), y), start = >>> > start, ?: >>> > ?error in evaluating the argument 'x' in selecting a method for >>> > function 'gaps' >>> > >>> > R> sessionInfo() >>> > R version 2.12.0 beta (2010-09-30 r53084) >>> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> > >>> > locale: >>> > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> > >>> > attached base packages: >>> > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> > >>> > other attached packages: >>> > [1] GenomicRanges_1.1.36 IRanges_1.7.39 >>> > >>> > -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 >>> > >>> >>> >>> >>> -- >>> 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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- 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