IRanges-class            package:IRanges            R Documentation

IRanges and NormalIRanges objects

Description:

     The IRanges class is a simple implementation of the Ranges
     container where 2 integer vectors of the same length are used to
     store the start and width values. See the Ranges virtual class for
     a formal definition of Ranges objects and for their methods (all
     of them should work for IRanges objects).

     Some subclasses of the IRanges class are: NormalIRanges, Views,
     etc...

     A NormalIRanges object is just an IRanges object that is
     guaranteed to be "normal". See the Normality section in the man
     page for Ranges objects for the definition and properties of
     "normal" Ranges objects.

Constructor:

     See '?`IRanges-constructor`'.

Coercion:


      'as(from, "IRanges")': Creates an IRanges instance from a Ranges
          object, logical vector, or integer vector. When 'from' is a
          logical vector, the resulting IRanges object contains the
          indices for the runs of 'TRUE' values. When 'from' is an
          integer vector, the elements are either singletons or
          "increase by 1" sequences.

      'as(from, "NormalIRanges")': Creates a NormalIRanges instance
          from a logical or integer vector. When 'from' is an integer
          vector, the elements must be strictly increasing.


Methods for NormalIRanges objects:


      'max(x)': The maximum value in the finite set of integers
          represented by 'x'.

      'min(x)': The minimum value in the finite set of integers
          represented by 'x'.


Author(s):

     H. Pages

See Also:

     Ranges-class, Ranges-utils, IRanges-constructor, IRanges-utils,
     IRanges-setops.

     Some direct subclasses of the IRanges class (other than
     NormalIRanges): Views-class.

Examples:

       showClass("IRanges")  # shows (some of) the known subclasses

       ## ---------------------------------------------------------------------
       ## A. MANIPULATING IRanges OBJECTS
       ## ---------------------------------------------------------------------
       ## All the methods defined for Ranges objects work on IRanges objects.
       ## See ?Ranges for some examples.
       ## Also see ?`IRanges-utils` and ?`IRanges-setops` for additional
       ## operations on IRanges objects.

       ## ---------------------------------------------------------------------
       ## B. A NOTE ABOUT PERFORMANCE
       ## ---------------------------------------------------------------------
       ## Using an IRanges object for storing a big set of ranges is more
       ## efficient than using a standard R data frame:
       N <- 2000000L  # nb of ranges
       W <- 180L      # width of each range
       start <- 1L
       end <- 50000000L
       set.seed(777)
       range_starts <- sort(sample(end-W+1L, N))
       range_widths <- rep.int(W, N)
       ## Instantiation is faster
       system.time(x <- IRanges(start=range_starts, width=range_widths))
       system.time(y <- data.frame(start=range_starts, width=range_widths))
       ## Subsetting is faster
       system.time(x16 <- x[c(TRUE, rep.int(FALSE, 15))])
       system.time(y16 <- y[c(TRUE, rep.int(FALSE, 15)), ])
       ## Internal representation is more compact
       object.size(x16)
       object.size(y16)

