Views-utils {IRanges}R Documentation

Utility functions and numeric summary of Views of numerics

Description

The slice function creates a Views object that contains the indices where the data are within the specified bounds.

The viewMins, viewMaxs, viewSums functions calculate the minimums, maximums, and sums on views respectively.

Usage

  slice(x, lower=-Inf, upper=Inf, ...)

  viewMins(x, na.rm=FALSE)
  viewMaxs(x, na.rm=FALSE)
  viewSums(x, na.rm=FALSE)

Arguments

x An XRleInteger, XInteger object or an integer vector for slice.
An XRleIntegerViews, XIntegerViews object for viewMins, viewMaxs and viewSums.
lower, upper The lower and upper bounds for the slice.
na.rm Logical indicating whether or not to include missing values in the results.
... Additional arguments to be passed to or from methods.

Details

The slice function creates views on XRleInteger or XInteger objects where the data are within the specified bounds. This is useful for finding areas of absolute maxima (peaks), absolute minima (troughs), or fluxuations within a specified limits.

The viewMins, viewMaxs, and viewSums functions provide efficient methods for calculating the specified numeric summary by performing the looping in compiled code.

Value

An XRleIntegerViews or XIntegerViews object for slice.
An integer vector of length(x) containing the numeric summaries for the views.

Author(s)

P. Aboyoun

See Also

XRleIntegerViews-class, XIntegerViews-class

Examples

  ## Views derived from vector
  vec <- as.integer(c(19, 5, 0, 8, 5))
  slice(vec, lower=5, upper=8)

  set.seed(0)
  vec <- sample(24)
  vecViews <- slice(vec, lower=4, upper=16)
  vecViews
  viewMins(vecViews)
  viewMaxs(vecViews)
  viewSums(vecViews)

  ## Views derived from coverage
  x <- IRanges(start=c(1L, 9L, 4L, 1L, 5L, 10L),
               width=c(5L, 6L, 3L, 4L, 3L,  3L))
  coverage(x, start=1, end=15)

[Package IRanges version 1.0.16 Index]