IRanges (version 2.6.0)

IRanges-constructor: The IRanges constructor and supporting functions

Description

The IRanges function is a constructor that can be used to create IRanges instances.

solveUserSEW0 and solveUserSEW are utility functions that solve a set of user-supplied start/end/width values.

Usage

## IRanges constructor:
IRanges(start=NULL, end=NULL, width=NULL, names=NULL)
## Supporting functions (not for the end user):
solveUserSEW0(start=NULL, end=NULL, width=NULL)
solveUserSEW(refwidths, start=NA, end=NA, width=NA,
             rep.refwidths=FALSE,
             translate.negative.coord=TRUE,
             allow.nonnarrowing=FALSE)

Arguments

start, end, width

For IRanges and solveUserSEW0: NULL, or vector of integers (eventually with NAs).

For solveUserSEW: vector of integers (eventually with NAs).

names

A character vector or NULL.

refwidths

Vector of non-NA non-negative integers containing the reference widths.

rep.refwidths

TRUE or FALSE. Use of rep.refwidths=TRUE is supported only when refwidths is of length 1.

translate.negative.coord, allow.nonnarrowing

TRUE or FALSE.

See Also

IRanges-class, narrow

Examples

## ---------------------------------------------------------------------
  ## A. USING THE IRanges() CONSTRUCTOR
  ## ---------------------------------------------------------------------
  IRanges(start=11, end=rep.int(20, 5))
  IRanges(start=11, width=rep.int(20, 5))
  IRanges(-2, 20)  # only one range
  IRanges(start=c(2, 0, NA), end=c(NA, NA, 14), width=11:0)
  IRanges()  # IRanges instance of length zero
  IRanges(names=character())

  ## With logical input:
  x <- IRanges(c(FALSE, TRUE, TRUE, FALSE, TRUE))  # logical vector input
  isNormal(x)  # TRUE
  x <- IRanges(Rle(1:30) %% 5 <= 2)  # logical Rle input
  isNormal(x)  # TRUE

  ## ---------------------------------------------------------------------
  ## B. USING solveUserSEW()
  ## ---------------------------------------------------------------------
  refwidths <- c(5:3, 6:7)
  refwidths

  solveUserSEW(refwidths)
  solveUserSEW(refwidths, start=4)
  solveUserSEW(refwidths, end=3, width=2)
  solveUserSEW(refwidths, start=-3)
  solveUserSEW(refwidths, start=-3, width=2)
  solveUserSEW(refwidths, end=-4)

  ## The start/end/width arguments are recycled:
  solveUserSEW(refwidths, start=c(3, -4, NA), end=c(-2, NA))

  ## Using 'rep.refwidths=TRUE':
  solveUserSEW(10, start=-(1:6), rep.refwidths=TRUE)
  solveUserSEW(10, end=-(1:6), width=3, rep.refwidths=TRUE)