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 1.2.3 Index]