Rle-utils: Common operations on Rle objects
In Bioconductor/S4Vectors: Foundation of vector-like and list-like containers in Bioconductor

Rle-utils

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 NAs when na.rm = TRUE.

pmin(..., na.rm = FALSE), pmin.int(..., na.rm = FALSE):

Parallel minima of the Rle input values. Removes NAs 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 NAs 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 NAs 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 NAs when na.rm = TRUE.

median(x, na.rm = FALSE):

Calculates the median of x. Removes NAs 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 NAs 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 NAs 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 NAs 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

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)

Bioconductor/S4Vectors documentation built on Nov. 2, 2024, 4:34 p.m.