Ranges-comparison {IRanges}R Documentation

Comparing and ordering ranges

Description

Methods for comparing and ordering the elements in one or more Ranges objects.

Usage

## ==== Equality and related methods ====
## --------------------------------------

## S4 method for signature 'Ranges,Ranges'
e1 == e2

## S4 method for signature 'Ranges,Ranges'
e1 != e2

## S4 method for signature 'Ranges'
duplicated(x, incomparables=FALSE, fromLast=FALSE,
           method=c("auto", "quick", "hash"), ...)

## S4 method for signature 'Ranges'
unique(x, incomparables=FALSE, fromLast=FALSE,
       method=c("auto", "quick", "hash"), ...)

## ==== Ordering and related methods ====
## --------------------------------------

## S4 method for signature 'Ranges,Ranges'
e1 <= e2
## S4 method for signature 'Ranges,Ranges'
e1 >= e2
## S4 method for signature 'Ranges,Ranges'
e1 < e2
## S4 method for signature 'Ranges,Ranges'
e1 > e2

## S4 method for signature 'Ranges'
order(..., na.last=TRUE, decreasing=FALSE)

## S4 method for signature 'Ranges'
sort(x, decreasing=FALSE, ...)

## S4 method for signature 'Ranges'
rank(x, na.last=TRUE,
     ties.method=c("average", "first", "random", "max", "min"))

## ==== Generalized range-wise comparison ====
## -------------------------------------------
compare(x, y)
rangeComparisonCodeToLetter(code)

Arguments

e1, e2, x, y

Ranges objects.

incomparables

Must be FALSE.

fromLast

See default S3 method for duplicated.

method

Use a Quicksort-based (method="quick") or a hash-based (method="hash") algorithm. The latter tends to give better performance, except maybe for some pathological input that we've not been able to determine so far. When method="auto" is specified, the hash-based algorithm is used as long as the length of x is <= 2^29, otherwise the Quicksort-based algorithm is used.

...

Ranges objects for order.

na.last

Ignored.

decreasing

TRUE or FALSE.

ties.method

A character string specifying how ties are treated. Only "first" is supported for now.

code

A vector of codes as returned by compare.

Details

Two ranges are considered equal iff they share the same start and width. Note that with this definition, 2 empty ranges are generally not equal (they need to share the same start to be considered equal). This means that, when it comes to comparing ranges, an empty range is interpreted as a position between its end and start. For example, a typical usecase is comparison of insertion points defined along a string (like a DNA sequence) and represented as empty ranges.

Ranges are ordered by starting position first, and then by width. This way, the space of ranges is totally ordered. The order, sort and rank methods for Ranges objects are consistent with this order.

duplicated(x): Determines which elements of x are equal to elements with smaller subscripts, and returns a logical vector indicating which elements are duplicates. It is semantically equivalent to duplicated(as.data.frame(x)). See duplicated in the base package for more details.

unique(x): Removes duplicate ranges from x. See unique in the base package for more details.

order(...): Returns a permutation which rearranges its first argument (a Ranges object) into ascending order, breaking ties by further arguments (also Ranges objects). See order in the BiocGenerics package for more information.

sort(x): Sorts x. See sort in the base package for more details.

rank(x, na.last=TRUE, ties.method=c("average", "first", "random", "max", "min")): Returns the sample ranks of the ranges in x. See rank in the base package for more details.

compare(x, y): Performs "generalized range-wise comparison" of x and y, that is, returns an integer vector where the i-th element is a code describing how the i-th element in x is qualitatively positioned relatively to the i-th element in y.

Here is a summary of the 13 predefined codes and their meanings:

        -6: x[i]: .oooo.......         6: x[i]: .......oooo.
            y[i]: .......oooo.            y[i]: .oooo.......

        -5: x[i]: ..oooo......         5: x[i]: ......oooo..
            y[i]: ......oooo..            y[i]: ..oooo......

        -4: x[i]: ...oooo.....         4: x[i]: .....oooo...
            y[i]: .....oooo...            y[i]: ...oooo.....

        -3: x[i]: ...oooooo...         3: x[i]: .....oooo...
            y[i]: .....oooo...            y[i]: ...oooooo...

        -2: x[i]: ..oooooooo..         2: x[i]: ....oooo....
            y[i]: ....oooo....            y[i]: ..oooooooo..

        -1: x[i]: ...oooo.....         1: x[i]: ...oooooo...
            y[i]: ...oooooo...            y[i]: ...oooo.....

                        0: x[i]: ...oooooo...
                           y[i]: ...oooooo...
      
Note that this way of comparing ranges is a refinement over the standard ranges comparison defined by the ==, !=, <=, >=, < and > operators. In particular a code that is < 0, = 0, or > 0, corresponds to x[i] < y[i], x[i] == y[i], or x[i] > y[i], respectively. The compare method for Ranges objects is guaranteed to return predefined codes only but methods for other objects (e.g. for GenomicRanges objects) can return non-predefined codes. Like for the predefined codes, the sign of any non-predefined code must tell whether x[i] is less than, or greater than y[i].

rangeComparisonCodeToLetter(x): Translate the codes returned by compare. The 13 predefined codes are translated as follow: -6 -> a; -5 -> b; -4 -> c; -3 -> d; -2 -> e; -1 -> f; 0 -> g; 1 -> h; 2 -> i; 3 -> j; 4 -> k; 5-> l; 6 -> m. Any non-predefined code is translated to X. The translated codes are returned in a factor with 14 levels: a, b, ..., l, m, X.

See Also

Ranges-class, IRanges-class, duplicated, unique, order, sort, rank

Examples

  x <- IRanges(start=c(20L, 8L, 20L, 22L, 25L, 20L, 22L, 22L),
               width=c( 4L, 0L, 11L,  5L,  0L,  9L,  5L,  0L))
  x

  ## ---------------------------------------------------------------------
  ## A. EQUALITY AND RELATED METHODS
  ## ---------------------------------------------------------------------
  which(width(x) == 0)  # 3 empty ranges
  x[2] == x[2]  # TRUE
  x[2] == x[5]  # FALSE
  x == x[4]
  duplicated(x)
  unique(x)

  ## ---------------------------------------------------------------------
  ## B. ORDERING AND RELATED METHODS
  ## ---------------------------------------------------------------------
  x >= x[3]
  order(x)
  sort(x)
  rank(x, ties.method="first")

  ## ---------------------------------------------------------------------
  ## C. GENERALIZED RANGE-WISE COMPARISON OF 2 Ranges OBJECTS
  ## ---------------------------------------------------------------------
  x0 <- IRanges(1:11, width=4)
  x0
  y0 <- IRanges(6, 9)
  compare(x0, y0)
  compare(IRanges(4:6, width=6), y0)
  compare(IRanges(6:8, width=2), y0)
  compare(x0, y0) < 0   # equivalent to 'x0 < y0'
  compare(x0, y0) == 0  # equivalent to 'x0 == y0'
  compare(x0, y0) > 0   # equivalent to 'x0 > y0'

  rangeComparisonCodeToLetter(-10:10)
  rangeComparisonCodeToLetter(compare(x0, y0))

[Package IRanges version 1.14.4 Index]