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: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
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
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
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