Rle-utils {S4Vectors} | R Documentation

## Common operations on Rle objects

### Description

Common operations on Rle objects.

### Group Generics

Rle objects have support for S4 group generic functionality:

`Arith`

  `"+"`, `"-"`, `"*"`, `"^"`, `"%%"`, `"%/%"`, `"/"`

`Compare`

  `"=="`, `">"`, `"<"`, `"!="`, `"<="`, `">="`

`Logic`

  `"&"`, `"|"`

`Ops`

  `"Arith"`, `"Compare"`, `"Logic"`

`Math`

  `"abs"`, `"sign"`, `"sqrt"`, `"ceiling"`, `"floor"`, `"trunc"`, `"cummax"`, `"cummin"`, `"cumprod"`, `"cumsum"`, `"log"`, `"log10"`, `"log2"`, `"log1p"`, `"acos"`, `"acosh"`, `"asin"`, `"asinh"`, `"atan"`, `"atanh"`, `"exp"`, `"expm1"`, `"cos"`, `"cosh"`, `"sin"`, `"sinh"`, `"tan"`, `"tanh"`, `"gamma"`, `"lgamma"`, `"digamma"`, `"trigamma"`

`Math2`

  `"round"`, `"signif"`

`Summary`

  `"max"`, `"min"`, `"range"`, `"prod"`, `"sum"`, `"any"`, `"all"`

`Complex`

  `"Arg"`, `"Conj"`, `"Im"`, `"Mod"`, `"Re"`

See S4groupGeneric for more details.

### Summary

In the code snippets below, `x` is an Rle object:

  `summary(object, ..., digits = max(3, getOption("digits") - 3))`: Summarizes the Rle object using an atomic vector convention. The `digits` argument is used for number formatting with `signif()`.

### Logical Data Methods

In the code snippets below, `x` is an Rle object:

  `!x`: Returns logical negation (NOT) of `x`.

  `which(x)`: Returns an integer vector representing the `TRUE` indices of `x`.

### Numerical Data Methods

In the code snippets below, `x` is an Rle object:

  `diff(x, lag = 1, differences = 1`: Returns suitably lagged and iterated differences of `x`.

  `lag`

    An integer indicating which lag to use.

  `differences`

    An integer indicating the order of the difference.

  `pmax(..., na.rm = FALSE)`, `pmax.int(..., na.rm = FALSE)`: Parallel maxima of the Rle input values. Removes `NA`s when `na.rm = TRUE`.

  `pmin(..., na.rm = FALSE)`, `pmin.int(..., na.rm = FALSE)`: Parallel minima of the Rle input values. Removes `NA`s when `na.rm = TRUE`.

  `which.max(x)`: Returns the index of the first element matching the maximum value of `x`.

  `mean(x, na.rm = FALSE)`: Calculates the mean of `x`. Removes `NA`s when `na.rm = TRUE`.

  `var(x, y = NULL, na.rm = FALSE)`: Calculates the variance of `x` or covariance of `x` and `y` if both are supplied. Removes `NA`s when `na.rm = TRUE`.

  `cov(x, y, use = "everything")`, `cor(x, y, use = "everything")`: Calculates the covariance and correlation respectively of Rle objects `x` and `y`. The `use` argument is an optional character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings `"everything"`, `"all.obs"`, `"complete.obs"`, `"na.or.complete"`, or `"pairwise.complete.obs"`.

  `sd(x, na.rm = FALSE)`: Calculates the standard deviation of `x`. Removes `NA`s when `na.rm = TRUE`.

  `median(x, na.rm = FALSE)`: Calculates the median of `x`. Removes `NA`s when `na.rm = TRUE`.

  `quantile(x, probs = seq(0, 1, 0.25), na.rm = FALSE, names = TRUE, type = 7, ...)`: Calculates the specified quantiles of `x`.

  `probs`

    A numeric vector of probabilities with values in [0,1].

  `na.rm`

    If `TRUE`, removes `NA`s from `x` before the quantiles are computed.

  `names`

    If `TRUE`, the result has names describing the quantiles.

  `type`

    An integer between 1 and 9 selecting one of the nine quantile algorithms detailed in `quantile`.

  ...

    Further arguments passed to or from other methods.

  `mad(x, center = median(x), constant = 1.4826, na.rm = FALSE, low = FALSE, high = FALSE)`: Calculates the median absolute deviation of `x`.

  `center`

    The center to calculate the deviation from.

  `constant`

    The scale factor.

  `na.rm`

    If `TRUE`, removes `NA`s from `x` before the mad is computed.

  `low`

    If `TRUE`, compute the 'lo-median'.

  `high`

    If `TRUE`, compute the 'hi-median'.

  `IQR(x, na.rm = FALSE)`: Calculates the interquartile range of `x`.

  `na.rm`

    If `TRUE`, removes `NA`s from `x` before the IQR is computed.

  `smoothEnds(y, k = 3)`: Smooth end points of an Rle `y` using subsequently smaller medians and Tukey's end point rule at the very end.

  `k`

    An integer indicating the width of largest median window; must be odd.

### Character Data Methods

In the code snippets below, `x` is an Rle object:

  `nchar(x, type = "chars", allowNA = FALSE)`: Returns an integer Rle representing the number of characters in the corresponding values of `x`.

  `type`

    One of `c("bytes", "chars", "width")`.

  `allowNA`

    Should `NA` be returned for invalid multibyte strings rather than throwing an error?

  `substr(x, start, stop)`, `substring(text, first, last = 1000000L)`: Returns a character or factor Rle containing the specified substrings beginning at `start`/`first` and ending at `stop`/`last`.

  `chartr(old, new, x)`: Returns a character or factor Rle containing a translated version of `x`.

  `old`

    A character string specifying the characters to be translated.

  `new`

    A character string specifying the translations.

  `tolower(x)`: Returns a character or factor Rle containing a lower case version of `x`.

  `toupper(x)`: Returns a character or factor Rle containing an upper case version of `x`.

  `sub(pattern, replacement, x, ignore.case = FALSE, perl = FALSE, fixed = FALSE, useBytes = FALSE)`: Returns a character or factor Rle containing replacements based on matches determined by regular expression matching. See `sub` for a description of the arguments.

  `gsub(pattern, replacement, x, ignore.case = FALSE, perl = FALSE, fixed = FALSE, useBytes = FALSE)`: Returns a character or factor Rle containing replacements based on matches determined by regular expression matching. See `gsub` for a description of the arguments.

  `paste(..., sep = " ", collapse = NULL)`: Returns a character or factor Rle containing a concatenation of the values in `...`.

### Factor Data Methods

In the code snippets below, `x` is an Rle object:

  `levels(x)`, `levels(x) <- value`: Gets and sets the factor levels, respectively.

  `nlevels(x)`: Returns the number of factor levels.

  `droplevels(x)`: Drops unused factor levels.

### Author(s)

P. Aboyoun

### See Also

Rle objects

S4groupGeneric

### Examples

    x <- Rle(10:1, 1:10)
    x

    sqrt(x)
    x^2 + 2 * x + 1
    range(x)
    sum(x)
    mean(x)

    z <- c("the", "quick", "red", "fox", "jumps", "over", "the", "lazy", "brown", "dog")
    z <- Rle(z, seq_len(length(z)))
    chartr("a", "@", z)
    toupper(z)

[Package S4Vectors version 0.20.1 Index]