[BioC] unique, duplicated, order, etc... on a GRanges object

[Hervé Pagès]

Hi there,

Seems like there was some need for this.

So I added the standard set of methods for ordering and comparing
genomic ranges i.e. duplicated, unique, order, sort, rank, "==",
"!=", "<=", ">=", "<", ">" now all work with GRanges objects.
It's in GenomicRanges 1.4.8 (release) and 1.5.27 (devel).

With Steve's big GRanges object:

   > system.time(oo <- order(xgr))
      user  system elapsed
    18.600   0.370  19.007

'xgr' obtained with:

   N <- 20000000L  # nb of ranges
   W <- 40L        # average width of the ranges
   start <- 1L
   end <- 55000000L
   set.seed(777)
   x_start <- sample(end - W - 2L, N, replace=TRUE)
   x_width <- W + sample(-3:3, N, replace=TRUE)
   x <- IRanges(start=x_start, width=x_width)

   xgr <- GRanges(sample(c('chr1', 'chr2'), length(x), replace=TRUE), x,
                  sample(c('+', '-'), length(x), replace=TRUE))

You can have a look at ?`GenomicRanges-comparison` for more examples.

Let me know if you find any issue with this.

Cheers,
H.

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

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