[Bioc-sig-seq] Combine GRanges Stored In A GRangesList

Dario Strbenac D.Strbenac at garvan.org.au
Tue Nov 30 06:00:17 CET 2010


I have a GRangesList and some of the GRanges elements of it are replicates that I'd like to pool together. I can't get the c() to work with GRanges that are in a GRangesList.

> summary(IPlist)
     Length       Class        Mode 
          8 GRangesList          S4
> tmp <- do.call(c, IPlist[1:2])
Error in do.call(c, IPlist[1:2]) : second argument must be a list

Is there a smarter way of achieving my use case than using c() ? I've got GenomicRanges 1.2.1.

Note that it also doesn't work if I have a standard list of GRanges.

> tmpList <- as.list(IPlist)
> tmp <- do.call(c, tmpList[1:2])
> length(tmp)
[1] 2


Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010

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