Hi, On Tue, Nov 30, 2010 at 12:00 AM, Dario Strbenac <[email protected]> wrote: > Hello, > > 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
Try: R> do.call(c, unname(as.list(IPlist))) The names() of the GRangesList is likely getting in your way here. -steve -- 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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
