[BioC] suppressing reduce() function when applying set operations to GRanges

[Hervé Pagès]

Hi Bill,

On 02/10/2013 03:00 PM, Bill Gibb wrote:
> Hello,
>
> I noticed that when applying set operations to GRanges objects, the returned range is reduced (by default), e.g.
>
> 	r1 <- GRanges(seqnames=c(1,1,1), ranges=IRanges(start=c(1,3,5), end=c(1,3,5)), strand='*')
> 	length(r1)
> 	r2 <- GRanges(seqnames=c(1,1,1), ranges=IRanges(start=c(1,3,4), end=c(1,3,4)), strand='*')
> 	length(r2)
> 	r3 <- union(r1,r2)
> 	length(r3)
> 	sum(width(ranges(r3)))
>
> Both r1 and r2 have length 3, whereas r3 has length 2, due to the implicit reduce applied to the result of union(). I can see that reducing the ranges would normally be desired when applying set operations, however there are occasions when one might want to keep a list of singleton ranges (e.g. when sub-sampling at the genomic coordinate level). Is there a way to suppress the reduce() operation when applying set operations to GRanges?

You could do:

   > unique(c(r1, r2))
   GRanges with 4 ranges and 0 metadata columns:
       seqnames    ranges strand
            <Rle> <IRanges>  <Rle>
     [1]        1    [1, 1]      *
     [2]        1    [3, 3]      *
     [3]        1    [5, 5]      *
     [4]        1    [4, 4]      *
     ---
     seqlengths:
       1
      NA

which is another form of union() that is certainly more in the spirit
of what base::union() does on ordinary vectors.

However union(x, y) on GRanges objects goes one step further by reducing
the above result. Yes we could add the 'reduce.ranges' arg to control
this, considering that it's not the 1st time that users seem to be
confused by this.

Cheers,
H.


> Something like union(r1, r2, reduce.ranges=FALSE) would be nice.
>
> I also tried:
>
> 	resize(r3,width=1)
>
> however it appears to simply truncate multi-base sequences.
>
> Thank you.
>
> Bill Gibb
> Genomic Health, Inc.
> Redwood City, CA
>
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-- 
Hervé Pagès

Program in Computational Biology
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