[BioC] Bug (?) in IRanges::findOverlaps(self, ignoreSelf=TRUE, ignoreRedundat=TRUE)

[Steve Lianoglou]

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