query and subject hits in findOverlaps through different space names
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Robert Castelo ★ 3.2k
@rcastelo
Last seen 4 days ago
Barcelona/Universitat Pompeu Fabra
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..) 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
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@michael-lawrence-3846
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On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo <robert.castelo@upf.edu>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 > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Has this been fixed in svn? Michael Lawrence wrote: > On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo <robert.castelo at="" upf.edu="">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 >> 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 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- 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
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Yes this has been fixed. On Tue, Apr 13, 2010 at 7:24 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Has this been fixed in svn? > > Michael Lawrence wrote: > >> On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo <robert.castelo@upf.edu>> >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 >>> Bioconductor@stat.math.ethz.ch >>> 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 >> Bioconductor@stat.math.ethz.ch >> 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]]
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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" <lawrence.michael@gene.com> wrote: Yes this has been fixed. On Tue, Apr 13, 2010 at 7:24 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Has this been fixed in svn? > > Michael Lawrence wrote: > >> On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo <robert.castelo@upf.edu>> >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 >>> Bioconductor@stat.math.ethz.ch >>> 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 >> Bioconductor@stat.math.ethz.ch >> 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 Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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thanks Michael for fixing this quickly, one minor detail, i've noticed that the version number of the IRanges code i've checked out with the fix from the svn repository is 1.5.76 which is the same that showed up in the sessionInfo() below reporting the bug. maybe it is ok like this, but just wanted to point it out in case that it should be different for the automagic update.packages() thingy. cheers, robert. On 4/13/10 5:13 PM, Michael Lawrence wrote: > Yes this has been fixed. > > On Tue, Apr 13, 2010 at 7:24 AM, James W. MacDonald > <jmacdon at="" med.umich.edu="">wrote: > > >> Has this been fixed in svn? >> >> Michael Lawrence wrote: >> >> >>> On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo<robert.castelo at="" upf.edu="">>> >>>> 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 >>>> 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 >>>> >>>> >>>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> 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 >>> >>> >> -- >> 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 > 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 >
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On 04/13/2010 02:16 PM, Robert Castelo wrote: > thanks Michael for fixing this quickly, one minor detail, i've noticed > that the version > number of the IRanges code i've checked out with the fix from the svn > repository is > 1.5.76 which is the same that showed up in the sessionInfo() below > reporting the bug. > maybe it is ok like this, but just wanted to point it out in case that > it should be different > for the automagic update.packages() thingy. Hi Robert -- that must have been an oversight on Michael's part and I've bumped the version, thanks. Martin > > cheers, > robert. > > > On 4/13/10 5:13 PM, Michael Lawrence wrote: >> Yes this has been fixed. >> >> On Tue, Apr 13, 2010 at 7:24 AM, James W. MacDonald >> <jmacdon at="" med.umich.edu="">wrote: >> >> >>> Has this been fixed in svn? >>> >>> Michael Lawrence wrote: >>> >>> >>>> On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo<robert.castelo at="" upf.edu="">>>> >>>>> 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 >>>>> 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 >>>>> >>>>> >>>>> >>>> [[alternative HTML version deleted]] >>>> >>>> >>>> _______________________________________________ >>>> 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 >>>> >>>> >>> -- >>> 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 >> 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 >> > > _______________________________________________ > 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 -- 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
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