Dear ChiPpeakAnno users, There is a bug in IRanges which affected ChIPpeakAnno devel version since 2/26/10. So if you have used ChIPpeakAnno devel version released after 2/26/10, please download the most recent IRanges and ChIPpeakAnno from SVN and rerun the script. Sorry for the extra work.
Best regards, Julie On 4/13/10 11:13 AM, "Michael Lawrence" <[email protected]> wrote: Yes this has been fixed. On Tue, Apr 13, 2010 at 7:24 AM, James W. MacDonald <[email protected]>wrote: > Has this been fixed in svn? > > Michael Lawrence wrote: > >> On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo <[email protected] >> >wrote: >> >> dear list and, particularly, IRanges developers, >>> >>> i've noticed a change shown below in the functionality of the >>> findOverlap function from the IRanges package from the current BioC >>> release version 2.10 to the current BioC devel (about to become release) >>> version 2.11 (i've checked-out the latest IRanges version at the svn >>> repository). >>> >>> this change seems to alter the way in which findOverlaps() return the >>> hits. in the current release findOverlaps() was returning the index of >>> the hits with respect to the entire RangedData object while in the >>> current devel version it does it with respect to the corresponding >>> space. is this an intended change or is it a bug? (i was happier with >>> the behavior of the release..) >>> >>> >>> It's a bug. Dimensions got switched around in RangesMatching, which >> confused >> RangesMatchingList. It's been broken since 2/26/10, in case anyone wants >> to >> re-run their scripts. >> >> Thanks a lot for catching this, >> >> Michael >> >> >> thanks! >>> robert. >>> >>> =========================current release 2.10================== >>> suppressPackageStartupMessages(library(IRanges)) >>> >>> x <- RangedData(IRanges(start=c(1,6), end=c(5,10)), >>> space=c("chr1","chr2")) >>> x >>> RangedData with 2 rows and 0 value columns across 2 spaces >>> space ranges | >>> <character> <IRanges> | >>> 1 chr1 [1, 5] | >>> 2 chr2 [6, 10] | >>> >>> y <- RangedData(IRanges(start=8, end=10), >>> space="chr2") >>> y >>> RangedData with 1 row and 0 value columns across 1 space >>> space ranges | >>> <character> <IRanges> | >>> 1 chr2 [8, 10] | >>> >>> as.matrix(findOverlaps(x, y)) >>> query subject >>> [1,] 2 1 >>> sessionInfo() >>> R version 2.10.1 (2009-12-14) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] IRanges_1.4.14 >>> =============================================================== >>> >>> ========================current devel 2.11===================== >>> suppressPackageStartupMessages(library(IRanges)) >>> >>> x <- RangedData(IRanges(start=c(1,6), end=c(5,10)), >>> space=c("chr1","chr2")) >>> x >>> RangedData with 2 rows and 0 value columns across 2 spaces >>> space ranges | >>> <character> <IRanges> | >>> 1 chr1 [1, 5] | >>> 2 chr2 [6, 10] | >>> y <- RangedData(IRanges(start=8, end=10), >>> space="chr2") >>> y >>> RangedData with 1 row and 0 value columns across 1 space >>> space ranges | >>> <character> <IRanges> | >>> 1 chr2 [8, 10] | >>> as.matrix(findOverlaps(x, y)) >>> query subject >>> [1,] 1 1 >>> R version 2.11.0 Under development (unstable) (2010-02-25 r51180) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> [1] C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods >>> base >>> >>> other attached packages: >>> [1] IRanges_1.5.76 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
