[Bioc-devel] GRanges Intersect

Dario Strbenac D.Strbenac at garvan.org.au
Tue Sep 27 06:00:05 CEST 2011


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.

load(url("")) # 90 KB
a                     # 13710 ranges
unique(a)             # 13710 ranges
intersect(a, a)       # 12689 ranges

My setup is :

R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-mingw32/x64 (64-bit)

[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

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