[Bioc-devel] GRanges Intersect

[Martin Morgan]

On 09/26/2011 09:00 PM, Dario Strbenac wrote:
> Hello,
>
> There seems to be some unexpected behaviour in intersect(). When I intersect a GRanges with itself, I'd expect that the result has the same length as the input GRanges. All of the ranges are unique.
>
> Here is an example that illustrates it.
>
> library(GenomicRanges)
> load(url("http://129.94.136.7/file_dump/dario/a.obj")) # 90 KB
> a                     # 13710 ranges
> unique(a)             # 13710 ranges
> intersect(a, a)       # 12689 ranges

Hi Dario -- some overlap

 > length(reduce(a))
[1] 12689

so like

 > (b = IRanges(5, c(10, 15)))
IRanges of length 2
     start end width
[1]     5  10     6
[2]     5  15    11
 > intersect(b, b)
IRanges of length 1
     start end width
[1]     5  15    11

Compare with ?pintersect and the 'Normality' section of ?Ranges.

Martin

>
> My setup is :
>
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.4.8 IRanges_1.10.6
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


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