On 07/25/2013 11:32 PM, Maintainer wrote:
Hi Jianhong, On 07/24/2013 08:18 AM, Ou, Jianhong wrote:Dear Hervé, Is it possible to ignore minoverlap when people set maxgap greater than 0 and give a message for that?That would make sense to me but we're probably overlooking something because Michael has a unit test where 'minoverlap' and 'maxgap' are used together: query <- IRanges(c(1, 5, 3, 4), width=c(2, 2, 4, 6)) subject <- IRanges(c(1, 3, 5, 6), width=c(4, 4, 5, 4)) tree <- IntervalTree(subject) result <- findOverlaps(query, tree, type = "start", maxgap = 1L, minoverlap = 3L) > result Hits of length 3 queryLength: 4 subjectLength: 4 queryHits subjectHits <integer> <integer> 1 3 2 2 4 2 3 4 3 This 'result' is what the unit test expects so we would need to understand what the meaning of using those 2 arguments together is (the man page is not really clear about it).
Checking again and paying more attention to the man page, 'maxgap' has a special meaning when 'type' is not "any". If type="start" it specifies the maximum difference in the starts. So I guess the question that remains is what to do with 'minoverlap' when type="any" and 'maxgap' is set to a value greater than 0. I'm OK with your proposal of ignoring it with a warning (unless the user also specifies 'minoverlap=0L', then no warning of course). H.
Michael? Thanks, H.Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 On 7/23/13 5:35 PM, "Hervé Pagès" <hpa...@fhcrc.org> wrote:Hi, This fails in Bioc-devel only and the following fix "seems" to address the problem: hpages@thinkpad:~/svn/bioconductor/Rpacks/IRanges$ svn diff R/findOverlaps-methods.R Index: R/findOverlaps-methods.R =================================================================== --- R/findOverlaps-methods.R (revision 78801) +++ R/findOverlaps-methods.R (working copy) @@ -142,7 +142,7 @@ # preprocess query preprocRes <- .preProcess_findOverlaps_query(query, maxgap, minoverlap) origQuery <- preprocRes$origQuery - unsortedQuery <- preprocRes$origQuery + unsortedQuery <- preprocRes$unsortedQuery query <- preprocRes$query query_ord <- preprocRes$query_ord However a *real* fix would be to actually clarify what's the meaning of using 'maxgap' and 'minoverlap' together. Right now the result below doesn't make much sense to me (using Bioc-release): > findOverlaps(IRanges(1, 5), IRanges(7, 10), maxgap=3, minoverlap=2) Hits of length 0 queryLength: 1 subjectLength: 1 > findOverlaps(IRanges(1, 5), IRanges(7, 10), maxgap=4, minoverlap=2) Hits of length 1 queryLength: 1 subjectLength: 1 queryHits subjectHits <integer> <integer> 1 1 1 H. On 07/23/2013 12:08 PM, Maintainer wrote:Hi, I got "negative widths are not allowed" error when I use findOverlaps. Could anybody help me to figure this out? Thanks. Here is the code: > library("IRanges") Loading required package: BiocGenerics Loading required package: parallel Attaching package: ŒBiocGenerics¹ The following objects are masked from Œpackage:parallel¹: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from Œpackage:stats¹: xtabs The following objects are masked from Œpackage:base¹: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist > Ranges1 <- sort(IRanges(start=c(3123260, 167889600), end=c(3123360, 167893599), names=c("Site5", "Site12"))) > Ranges2 <- sort(IRanges(start=c(312326, 3123260, 167888600), end=c(312586, 3123470, 167888999), names=c("t11", "t5", "t17"))) > tree = IntervalTree(Ranges2) > findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20, select = "first") Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : solving row 2: negative widths are not allowed > traceback() 11: .Call(.NAME, ..., PACKAGE = PACKAGE) 10: .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") 9: solveUserSEW0(start = start, end = end, width = width) 8: IRanges(pmax.int(qstart, sstart), pmin.int(send, qend)) 7: .local(x, ...) 6: ranges(result, unsortedQuery, subject) 5: ranges(result, unsortedQuery, subject) 4: .postProcess_findOverlaps_result(result, unsortedQuery, origQuery, subject, type, minoverlap, maxgap, origSelect) 3: .local(query, subject, maxgap, minoverlap, type, select, ...) 2: findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20, select = "first") 1: findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20, select = "first") > sessionInfo() R Under development (unstable) (2013-04-30 r62697) Platform: x86_64-apple-darwin12.3.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] IRanges_1.19.19 BiocGenerics_0.7.3 loaded via a namespace (and not attached): [1] stats4_3.1.0 Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 ________________________________________________________________________ devteam-bioc mailing list To unsubscribe from this mailing list send a blank email to devteam-bioc-le...@lists.fhcrc.org You can also unsubscribe or change your personal options at https://lists.fhcrc.org/mailman/listinfo/devteam-bioc-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
