Vector-comparison {S4Vectors} | R Documentation

## Compare, order, tabulate vector-like objects

### Description

Generic functions and methods for comparing, ordering, and tabulating vector-like objects.

### Usage

    ## Element-wise (aka "parallel") comparison of 2 Vector objects
    ## ------------------------------------------------------------

    pcompare(x, y)

    ## S4 method for signature 'Vector,Vector'
    e1 == e2
    ## S4 method for signature 'Vector,ANY'
    e1 == e2
    ## S4 method for signature 'ANY,Vector'
    e1 == e2

    ## S4 method for signature 'Vector,Vector'
    e1 <= e2
    ## S4 method for signature 'Vector,ANY'
    e1 <= e2
    ## S4 method for signature 'ANY,Vector'
    e1 <= e2

    ## S4 method for signature 'Vector,Vector'
    e1 != e2
    ## S4 method for signature 'Vector,ANY'
    e1 != e2
    ## S4 method for signature 'ANY,Vector'
    e1 != e2

    ## S4 method for signature 'Vector,Vector'
    e1 >= e2
    ## S4 method for signature 'Vector,ANY'
    e1 >= e2
    ## S4 method for signature 'ANY,Vector'
    e1 >= e2

    ## S4 method for signature 'Vector,Vector'
    e1 < e2
    ## S4 method for signature 'Vector,ANY'
    e1 < e2
    ## S4 method for signature 'ANY,Vector'
    e1 < e2

    ## S4 method for signature 'Vector,Vector'
    e1 > e2
    ## S4 method for signature 'Vector,ANY'
    e1 > e2
    ## S4 method for signature 'ANY,Vector'
    e1 > e2

    ## sameAsPreviousROW()
    ## -------------------

    sameAsPreviousROW(x)

    ## match()
    ## -------

    ## S4 method for signature 'Vector,Vector'
    match(x, table, nomatch = NA_integer_,
        incomparables = NULL, ...)

    ## selfmatch()
    ## -----------

    selfmatch(x, ...)

    ## duplicated() & unique()
    ## -----------------------

    ## S4 method for signature 'Vector'
    duplicated(x, incomparables=FALSE, ...)

    ## S4 method for signature 'Vector'
    unique(x, incomparables=FALSE, ...)

    ## %in%
    ## ----

    ## S4 method for signature 'Vector,Vector'
    x %in% table
    ## S4 method for signature 'Vector,ANY'
    x %in% table
    ## S4 method for signature 'ANY,Vector'
    x %in% table

    ## findMatches() & countMatches()
    ## ------------------------------

    findMatches(x, table, select=c("all", "first", "last"), ...)
    countMatches(x, table, ...)

    ## sort()
    ## ------

    ## S4 method for signature 'Vector'
    sort(x, decreasing=FALSE, na.last=NA, by)

    ## rank()
    ## ------

    ## S4 method for signature 'Vector'
    rank(x, na.last = TRUE, ties.method = c("average",
            "first", "last", "random", "max", "min"), by)

    ## xtfrm()
    ## -------

    ## S4 method for signature 'Vector'
    xtfrm(x)

    ## table()
    ## -------

    ## S4 method for signature 'Vector'
    table(...)

### Arguments

`x, y, e1, e2, table` | Vector-like objects.
`nomatch` | See `?base::match`.
`incomparables` | The `duplicated` method for Vector objects does NOT support this argument. The `unique` method for Vector objects, which is implemented on top of `duplicated`, propagates this argument to its call to `duplicated`. See `?base::duplicated` and `?base::unique` for more information about this argument for these generics. The `match` method for Vector objects does support this argument, see `?base::match` for details.
`select` | Only `select="all"` is supported at the moment. Note that you can use `match` if you want to do `select="first"`. Otherwise you're welcome to request this on the Bioconductor mailing list.
`ties.method` | See `?base::rank`.
`decreasing, na.last` | See `?base::sort`.
`by` | A formula referencing the metadata columns by which to sort, e.g., `~ x + y` sorts by column “x”, breaking ties with column “y”.
`...` | A Vector object for `table` (the `table` method for Vector objects can only take one input object). Otherwise, extra arguments supported by specific methods. In particular: The default `selfmatch` method, which is implemented on top of `match`, propagates the extra arguments to its call to `match`. The `duplicated` method for Vector objects, which is implemented on top of `selfmatch`, accepts extra argument `fromLast` and propagates the other extra arguments to its call to `selfmatch`. See `?base::duplicated` for more information about this argument. The `unique` method for Vector objects, which is implemented on top of `duplicated`, propagates the extra arguments to its call to `duplicated`. The default `findMatches` and `countMatches` methods, which are implemented on top of `match` and `selfmatch`, propagate the extra arguments to their calls to `match` and `selfmatch`. The `sort` method for Vector objects, which is implemented on top of `order`, only accepts extra argument `na.last` and propagates it to its call to `order`.

### Details

Doing `pcompare(x, y)` on 2 vector-like objects `x` and `y` of length 1 must return an integer less than, equal to, or greater than zero if the single element in `x` is considered to be respectively less than, equal to, or greater than the single element in `y`. If `x` or `y` have a length != 1, then they are typically expected to have the same length so `pcompare(x, y)` can operate element-wise, that is, in that case it returns an integer vector of the same length as `x` and `y` where the i-th element is the result of compairing `x[i]` and `y[i]`. If `x` and `y` don't have the same length and are not zero-length vectors, then the shortest is first recycled to the length of the longest. If one of them is a zero-length vector then `pcompare(x, y)` returns a zero-length integer vector.

`selfmatch(x, ...)` is equivalent to `match(x, x, ...)`. This is actually how the default `ANY` method is implemented. However note that the default `selfmatch(x, ...)` for Vector `x` will typically be more efficient than `match(x, x, ...)`, and can be made even more so if a specific `selfmatch` method is implemented for a given subclass.

`findMatches` is an enhanced version of `match` which, by default (i.e. if `select="all"`), returns all the matches in a Hits object.

`countMatches` returns an integer vector of the length of `x` containing the number of matches in `table` for each element in `x`.

### Value

For `pcompare`: see Details section above.

For `sameAsPreviousROW`: a logical vector of length equal to `x`, indicating whether each entry of `x` is equal to the previous entry. The first entry is always `FALSE` for a non-zero-length `x`.

For `match` and `selfmatch`: an integer vector of the same length as `x`.

For `duplicated`, `unique`, and `%in%`: see `?BiocGenerics::duplicated`, `?BiocGenerics::unique`, and `?`%in%``.

For `findMatches`: a Hits object by default (i.e. if `select="all"`).

For `countMatches`: an integer vector of the length of `x` containing the number of matches in `table` for each element in `x`.

For `sort`: see `?BiocGenerics::sort`.

For `xtfrm`: see `?base::xtfrm`.

For `table`: a 1D array of integer values promoted to the `"table"` class. See `?BiocGeneric::table` for more information.

### Note

The following notes are for developers who want to implement comparing, ordering, and tabulating methods for their own Vector subclass.

Subclass comparison methods can be split into various categories. The first category must be implemented for each subclass, as these do not have sensible defaults for arbitrary Vector objects:

- The S4Vectors package provides no `order` method for Vector objects. So calling `order` on a Vector derivative for which no specific `order` method is defined will use `base::order`, which calls `xtfrm`, with in turn calls `order`, which calls `xtfrm`, and so on. This infinite recursion of S4 dispatch eventually results in an error about reaching the stack limit.

  To avoid this behavior, a specialized `order` method needs to be implemented for specific Vector subclasses (e.g. for Hits and IntegerRanges objects).

- `sameAsPreviousROW` is default implemented on top of the `==` method, so will work out-of-the-box on Vector objects for which `==` works as expected. However, `==` is default implemented on top of `pcompare`, which itself has a default implementation that relies on `sameAsPreviousROW`! This again leads to infinite recursion and an error about the stack limit.

  To avoid this behavior, a specialized `sameAsPreviousROW` method must be implemented for specific Vector subclasses.

The second category contains methods that have default implementations provided for all Vector objects and their derivatives. These methods rely on the first category to provide sensible default behaviour without further work from the developer. However, it is often the case that greater efficiency can be achieved for a specific data structure by writing a subclass-specific version of these methods.

- The `pcompare` method for Vector objects is implemented on top of `order` and `sameAsPreviousROW`, and so will work out-of-the-box on Vector derivatives for which `order` and `sameAsPreviousROW` work as expected.

- The `xtfrm` method for Vector objects is also implemented on top of `order` and `sameAsPreviousROW`, and so will also work out-of-the-box on Vector derivatives for which `order` and `sameAsPreviousROW` work as expected.

- `selfmatch` is itself implemented on top of `xtfrm` (indirectly, via `grouping`) so it will work out-of-the-box on Vector objects for which `xtfrm` works as expected.

- The `match` method for Vector objects is implemented on top of `selfmatch`, so works out-of-the-box on Vector objects for which `selfmatch` works as expected.

(A careful reader may notice that `xtfrm` and `order` could be swapped between categories to achieve the same effect. Similarly, `sameAsPreviousROW` and `pcompare` could also be swapped. The exact categorization of these methods is left to the discretion of the developer, though this is mostly academic if both choices are specialized.)

The third category also contains methods that have default implementations, but unlike the second category, these defaults are straightforward and generally do not require any specialization for efficiency purposes.

- The 6 traditional binary comparison operators are: `==`, `!=`, `<=`, `>=`, `<`, and `>`. The S4Vectors package provides the following methods for these operators:

      setMethod("==", c("Vector", "Vector"),
          function(e1, e2) { pcompare(e1, e2) == 0L }
      )
      setMethod("<=", c("Vector", "Vector"),
          function(e1, e2) { pcompare(e1, e2) <= 0L }
      )
      setMethod("!=", c("Vector", "Vector"),
          function(e1, e2) { !(e1 == e2) }
      )
      setMethod(">=", c("Vector", "Vector"),
          function(e1, e2) { e2 <= e1 }
      )
      setMethod("<", c("Vector", "Vector"),
          function(e1, e2) { !(e2 <= e1) }
      )
      setMethod(">", c("Vector", "Vector"),
          function(e1, e2) { !(e1 <= e2) }
      )

  With these definitions, the 6 binary operators work out-of-the-box on Vector objects for which `pcompare` works the expected way. If `pcompare` is not implemented, then it's enough to implement `==` and `<=` methods to have the 4 remaining operators (`!=`, `>=`, `<`, and `>`) work out-of-the-box.

- The `duplicated`, `unique`, and `%in%` methods for Vector objects are implemented on top of `selfmatch`, `duplicated`, and `match`, respectively, so they work out-of-the-box on Vector objects for which `selfmatch`, `duplicated`, and `match` work the expected way.

- Also the default `findMatches` and `countMatches` methods are implemented on top of `match` and `selfmatch` so they work out-of-the-box on Vector objects for which those things work the expected way.

- The `sort` method for Vector objects is implemented on top of `order`, so it works out-of-the-box on Vector objects for which `order` works the expected way.

- The `table` method for Vector objects is implemented on top of `selfmatch`, `order`, and `as.character`, so it works out-of-the-box on a Vector object for which those things work the expected way.

### Author(s)

Hervé Pagès, with contributions from Aaron Lun

### See Also

- The Vector class.

- Hits-comparison for comparing and ordering hits.

- Vector-setops for set operations on vector-like objects.

- Vector-merge for merging vector-like objects.

- IntegerRanges-comparison in the IRanges package for comparing and ordering ranges.

- `==` and `%in%` in the base package, and `BiocGenerics::match`, `BiocGenerics::duplicated`, `BiocGenerics::unique`, `BiocGenerics::order`, `BiocGenerics::sort`, `BiocGenerics::rank` in the BiocGenerics package for general information about the comparison/ordering operators and functions.

- The Hits class.

- `BiocGeneric::table` in the BiocGenerics package.

### Examples

    ## ---------------------------------------------------------------------
    ## A. SIMPLE EXAMPLES
    ## ---------------------------------------------------------------------

    y <- c(16L, -3L, -2L, 15L, 15L, 0L, 8L, 15L, -2L)
    selfmatch(y)

    x <- c(unique(y), 999L)
    findMatches(x, y)
    countMatches(x, y)

    ## See ?`IntegerRanges-comparison` for more examples (on IntegerRanges
    ## objects). You might need to load the IRanges package first.

    ## ---------------------------------------------------------------------
    ## B. FOR DEVELOPERS: HOW TO IMPLEMENT THE BINARY COMPARISON OPERATORS
    ##    FOR YOUR Vector SUBCLASS
    ## ---------------------------------------------------------------------

    ## The answer is: don't implement them. Just implement pcompare() and the
    ## binary comparison operators will work out-of-the-box. Here is an
    ## example:

    ## (1) Implement a simple Vector subclass.

    setClass("Raw", contains="Vector", representation(data="raw"))

    setMethod("length", "Raw", function(x) length(x@data))

    setMethod("[", "Raw",
        function(x, i, j, ..., drop) { x@data <- x@data[i]; x }
    )

    x <- new("Raw", data=charToRaw("AB.x0a-BAA+C"))
    stopifnot(identical(length(x), 12L))
    stopifnot(identical(x[7:3], new("Raw", data=charToRaw("-a0x."))))

    ## (2) Implement a "pcompare" method for Raw objects.

    setMethod("pcompare", c("Raw", "Raw"),
        function(x, y) {as.integer(x@data) - as.integer(y@data)}
    )

    stopifnot(identical(which(x == x[1]), c(1L, 9L, 10L)))
    stopifnot(identical(x[x < x[5]], new("Raw", data=charToRaw(".-+"))))

[Package S4Vectors version 0.25.15 Index]