Rle-class: Rle objects

In S4Vectors: Foundation of vector-like and list-like containers in Bioconductor

Description

The Rle class is a general container for storing an atomic vector that is stored in a run-length encoding format. It is based on the rle function from the base package.

Constructor

Rle(values, lengths): This constructor creates an Rle instance out of an atomic vector or factor object values and an integer or numeric vector lengths with all positive elements that represent how many times each value is repeated. The length of these two vectors must be the same. lengths can be missing in which case values is turned into an Rle.

Getters

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

runLength(x): Returns the run lengths for x.

runValue(x): Returns the run values for x.

nrun(x): Returns the number of runs in x.

start(x): Returns the starts of the runs for x.

end(x): Returns the ends of the runs for x.

width(x): Same as runLength(x).

Setters

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

runLength(x) <- value: Replaces x with a new Rle object using run values runValue(x) and run lengths value.

runValue(x) <- value: Replaces x with a new Rle object using run values value and run lengths runLength(x).

Coercion

From atomic vector to Rle

In the code snippets below, from is an atomic vector:

as(from, "Rle"): This coercion creates an Rle instances out of an atomic vector from.

From Rle to other objects

In the code snippets below, x and from are Rle objects:

as.vector(x, mode="any"), as(from, "vector"): Creates an atomic vector based on the values contained in x. The vector will be coerced to the requested mode, unless mode is "any", in which case the most appropriate type is chosen.

as.factor(x), as(from, "factor"): Creates a factor object based on the values contained in x.

as.data.frame(x), as(from, "data.frame"): Creates a data.frame with a single column holding the result of as.vector(x).

decode(x): Converts an Rle to its native form, such as an atomic vector or factor. Calling decode on a non-Rle will return x by default, so it is generally safe for ensuring that an object is native.

General Methods

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

x[i, drop=getOption("dropRle", default=FALSE)]: Subsets x by index i, where i can be positive integers, negative integers, a logical vector of the same length as x, an Rle object of the same length as x containing logical values, or an IRanges object. When drop=FALSE returns an Rle object. When drop=TRUE, returns an atomic vector.

x[i] <- value: Replaces elements in x specified by i with corresponding elements in value. Supports the same types for i as x[i].

x %in% table: Returns a logical Rle representing set membership in table.

c(x, ..., ignore.mcols=FALSE): Concatenate Rle object x and the Rle objects in ... together. See ?c in this package (the S4Vectors package) for more information about concatenating Vector derivatives.

append(x, values, after = length(x)): Insert one Rle into another Rle.

values

the Rle to insert.

after

the subscript in x after which the values are to be inserted.

findRun(x, vec): Returns an integer vector indicating the run indices in Rle vec that are referenced by the indices in the integer vector x.

head(x, n = 6L): If n is non-negative, returns the first n elements of x. If n is negative, returns all but the last abs(n) elements of x.

is.na(x): Returns a logical Rle indicating which values are NA.

is.finite(x): Returns a logical Rle indicating which values are finite.

is.unsorted(x, na.rm = FALSE, strictly = FALSE): Returns a logical value specifying if x is unsorted.

na.rm

remove missing values from check.

strictly

check for _strictly_ increasing values.

length(x): Returns the underlying vector length of x.

match(x, table, nomatch = NA_integer_, incomparables = NULL): Matches the values in x to table:

table

the values to be matched against.

nomatch

the value to be returned in the case when no match is found.

incomparables

a vector of values that cannot be matched. Any value in x matching a value in this vector is assigned the nomatch value.

rep(x, times, length.out, each), rep.int(x, times): Repeats the values in x through one of the following conventions:

times

Vector giving the number of times to repeat each element if of length length(x), or to repeat the whole vector if of length 1.

length.out

Non-negative integer. The desired length of the output vector.

each

Non-negative integer. Each element of x is repeated each times.

rev(x): Reverses the order of the values in x.

show(object): Prints out the Rle object in a user-friendly way.

order(..., na.last=TRUE, decreasing=FALSE, method=c("auto", "shell", "radix")): Returns a permutation which rearranges its first argument into ascending or descending order, breaking ties by further arguments. See order.

sort(x, decreasing=FALSE, na.last=NA): Sorts the values in x.

decreasing

If TRUE, sort values in decreasing order. If FALSE, sort values in increasing order.

na.last

If TRUE, missing values are placed last. If FALSE, they are placed first. If NA, they are removed.

subset(x, subset): Returns a new Rle object made of the subset using logical vector subset.

table(...): Returns a table containing the counts of the unique values. Supported arguments include useNA with values of ‘no’ and ‘ifany’. Multiple Rle's must be concatenated with c() before calling table.

tabulate(bin, nbins = max(bin, 1L, na.rm = TRUE)): Just like tabulate, except optimized for Rle.

tail(x, n = 6L): If n is non-negative, returns the last n elements of x. If n is negative, returns all but the first abs(n) elements of x.

unique(x, incomparables = FALSE, ...): Returns the unique run values. The incomparables argument takes a vector of values that cannot be compared with FALSE being a special value that means that all values can be compared.

Set Operations

In the code snippets below, x and y are Rle object or some other vector-like object:

setdiff(x, y): Returns the unique elements in x that are not in y.

union(x, y): Returns the unique elements in either x or y.

intersect(x, y): Returns the unique elements in both x and y.

Author(s)

P. Aboyoun

See Also

Rle-utils, Rle-runstat, and aggregate for more operations on Rle objects.

rle

Vector-class

Examples

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

  runLength(x)
  runValue(x)
  nrun(x)

  diff(x)
  unique(x)
  sort(x)
  x[c(1,3,5,7,9)]
  x > 4

  x2 <- Rle(LETTERS[c(21:26, 25:26)], 8:1)
  table(x2)

  y <- Rle(c(TRUE,TRUE,FALSE,FALSE,TRUE,FALSE,TRUE,TRUE,TRUE))
  y
  as.vector(y)
  rep(y, 10)
  c(y, x > 5)

Example output

Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

integer-Rle of length 55 with 10 runs
  Lengths:  1  2  3  4  5  6  7  8  9 10
  Values : 10  9  8  7  6  5  4  3  2  1
 [1]  1  2  3  4  5  6  7  8  9 10
 [1] 10  9  8  7  6  5  4  3  2  1
[1] 10
integer-Rle of length 54 with 18 runs
  Lengths:  1  1  1  2  1  3  1  4  1  5  1  6  1  7  1  8  1  9
  Values : -1  0 -1  0 -1  0 -1  0 -1  0 -1  0 -1  0 -1  0 -1  0
 [1] 10  9  8  7  6  5  4  3  2  1
integer-Rle of length 55 with 10 runs
  Lengths: 10  9  8  7  6  5  4  3  2  1
  Values :  1  2  3  4  5  6  7  8  9 10
integer-Rle of length 5 with 4 runs
  Lengths:  1  1  1  2
  Values : 10  9  8  7
logical-Rle of length 55 with 2 runs
  Lengths:    21    34
  Values :  TRUE FALSE
x2
U V W X Y Z 
8 7 6 5 6 4 
logical-Rle of length 9 with 5 runs
  Lengths:     2     2     1     1     3
  Values :  TRUE FALSE  TRUE FALSE  TRUE
[1]  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE  TRUE
logical-Rle of length 90 with 41 runs
  Lengths:     2     2     1     1     5 ...     5     2     1     1     3
  Values :  TRUE FALSE  TRUE FALSE  TRUE ...  TRUE FALSE  TRUE FALSE  TRUE
logical-Rle of length 64 with 6 runs
  Lengths:     2     2     1     1    18    40
  Values :  TRUE FALSE  TRUE FALSE  TRUE FALSE

S4Vectors documentation built on Dec. 11, 2020, 2:02 a.m.