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).
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
