Hi, I think I've found a corner case in the findOverlaps function when you are: (i) omitting the subject arg (ii) both ignoreSelf and ignoreRedundant areTRUE (iii) and only 1 overlap should be returned(?) <-- not sure about this one Example: R> x <- IRanges(c(1, 10, 20), width=c(5, 11, 5)) R> findOverlaps(x, ignoreSelf=TRUE, ignoreRedundant=TRUE) Error in checkSlotAssignment(object, name, value) : assignment of an object of class "integer" is not valid for slot "matchMatrix" in an object of class "RangesMatching"; is(value, "matrix") is not TRUE It works, however, when ignoreSelf && ignoreReduncant == FALSE R> findOverlaps(x, ignoreRedundant=TRUE) ## this is fine R> findOverlaps(x, ignoreSelf=TRUE) ## also fine sessionInfo() R version 2.11.0 Patched (2010-05-05 r51909) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GenomeGraphs_1.8.0 biomaRt_2.4.0 bitops_1.0-4.1 Rsamtools_1.0.1 [5] BSgenome.Hsapiens.UCSC.hg18_1.3.16 BSgenome_1.16.1 GenomicRanges_1.0.1 RSQLite_0.8-4 [9] DBI_0.2-5 Biostrings_2.16.0 IRanges_1.6.1 loaded via a namespace (and not attached): [1] Biobase_2.8.0 GenomeAnnotations_0.1.1 RCurl_1.3-1 tools_2.11.0 XML_2.8-1 -- 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

Hi, On Wed, May 12, 2010 at 3:35 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi, > > I think I've found a corner case in the findOverlaps function when you are: > > (i) omitting the subject arg > (ii) both ignoreSelf and ignoreRedundant areTRUE > (iii) and only 1 overlap should be returned(?) <-- not sure about this one I think adding a judicious ",drop=FALSE]" in line112 IntervalTree-utils.R (rev 46808) would solve the problem, ie: mat <- mat[!duplicated(norm_mat),,drop=FALSE] -steve > > Example: > > R> x <- IRanges(c(1, 10, 20), width=c(5, 11, 5)) > R> findOverlaps(x, ignoreSelf=TRUE, ignoreRedundant=TRUE) > Error in checkSlotAssignment(object, name, value) : > ?assignment of an object of class "integer" is not valid for slot > "matchMatrix" in an object of class "RangesMatching"; is(value, > "matrix") is not TRUE > > It works, however, when ignoreSelf && ignoreReduncant == FALSE > > R> findOverlaps(x, ignoreRedundant=TRUE) ?## this is fine > R> findOverlaps(x, ignoreSelf=TRUE) ?## also fine > > sessionInfo() > R version 2.11.0 Patched (2010-05-05 r51909) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets > methods ? base > > other attached packages: > ?[1] GenomeGraphs_1.8.0 ? ? ? ? ? ? ? ? biomaRt_2.4.0 > ? ?bitops_1.0-4.1 ? ? ? ? ? ? ? ? ? ? Rsamtools_1.0.1 > ?[5] BSgenome.Hsapiens.UCSC.hg18_1.3.16 BSgenome_1.16.1 > ? ?GenomicRanges_1.0.1 ? ? ? ? ? ? ? ?RSQLite_0.8-4 > ?[9] DBI_0.2-5 ? ? ? ? ? ? ? ? ? ? ? ? ?Biostrings_2.16.0 > ? ?IRanges_1.6.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 ? ? ? ? ? GenomeAnnotations_0.1.1 RCurl_1.3-1 > ? ? tools_2.11.0 ? ? ? ? ? ?XML_2.8-1 > > -- > 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