Ranges-comparison {IRanges}R Documentation

Ranges comparison

Description

Equality and ordering of ranges, and related methods.

Usage

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

  x == y
  x != y

  ## S4 method for signature 'Ranges':
duplicated(x, incomparables=FALSE, fromLast=FALSE, ...)

  ## S4 method for signature 'Ranges':
unique(x, incomparables=FALSE, fromLast=FALSE, ...)

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

  x <= y
  x >= y
  x < y
  x > y

  ## 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"))

Arguments

x,y A Ranges object.
incomparables Must be FALSE.
fromLast TRUE or FALSE.
... 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.

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 base package for more details.
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.

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
  which(width(x) == 0)  # 3 empty ranges
  x[2] == x[2]  # TRUE
  x[2] == x[5]  # FALSE
  x == x[4]
  duplicated(x)
  unique(x)
  x >= x[3]
  order(x)
  sort(x)
  rank(x, ties.method="first")

[Package IRanges version 1.6.16 Index]