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

  viewApply(X, FUN, ..., simplify = TRUE)

  slice(x, lower=-Inf, upper=Inf, ...)
  ## S4 method for signature 'Rle':
  slice(x, lower=-Inf, upper=Inf,
                        includeLower=TRUE, includeUpper=TRUE)

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

  viewWhichMins(x, na.rm=FALSE)
  viewWhichMaxs(x, na.rm=FALSE)

  viewRangeMins(x, ...)
  viewRangeMaxs(x, ...)

Arguments

X A Views object.
FUN The function to be applied to each view in X.
... Additional arguments to be passed on.
simplify A logical value specifying whether or not the result should be simplified to a vector or matrix if possible.
x An Rle, XRleInteger, XInteger object or an integer vector for slice.
An RleViews, XRleIntegerViews, XIntegerViews object for viewMins, viewMaxs, and viewSums.
An Rle, XRleIntegerViews, XIntegerViews object for viewWhichMins and viewWhichMaxs.
lower, upper The lower and upper bounds for the slice.
includeLower, includeUpper Logical indicating whether or not the specified boundary is open or closed.
na.rm Logical indicating whether or not to include missing values in the results.

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.

The viewWhichMins, viewWhichMaxs, viewRangeMins, and viewRangeMaxs functions provide efficient methods for finding the location of the minimums and maximums.

Value

An XRleIntegerViews or XIntegerViews object for slice.
A vector of length(x) containing the numeric summaries for the views for viewMins, viewMaxs, viewSums, viewWhichMins, and viewWhichMaxs.
A IRanges object containing the location ranges for viewRangeMins and viewRangeMaxs.

Author(s)

P. Aboyoun

See Also

RleViews-class, XRleIntegerViews-class, XIntegerViews-class, which.min, colSums

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
  viewApply(vecViews, function(x) diff(as.integer(x)))
  viewMins(vecViews)
  viewMaxs(vecViews)
  viewSums(vecViews)
  viewWhichMins(vecViews)
  viewWhichMaxs(vecViews)

  ## Views derived from coverage
  x <- IRanges(start=c(1L, 9L, 4L, 1L, 5L, 10L),
               width=c(5L, 6L, 3L, 4L, 3L,  3L))
  slice(coverage(x), lower=2)

[Package IRanges version 1.2.0 Index]