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[Bioc-devel] GRanges Intersect

3 messages · Dario Strbenac, Martin Morgan

Original
Dario Strbenac
# 
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

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
Martin Morgan
#
On 09/26/2011 09:00 PM, Dario Strbenac wrote:
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