Vector-comparison: 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)
## S3 method for class 'Vector,Vector':
==(e1, e2)
## S3 method for class 'Vector,ANY':
==(e1, e2)
## S3 method for class 'ANY,Vector':
==(e1, e2)
## S3 method for class 'Vector,Vector':
<=(e1, e2)="" ##="" s3="" method="" for="" class="" 'vector,any':="" <="(e1," 'any,vector':="" e2)<="" p="">
## S3 method for class 'Vector,Vector':
!=(e1, e2)
## S3 method for class 'Vector,ANY':
!=(e1, e2)
## S3 method for class 'ANY,Vector':
!=(e1, e2)
## S3 method for class 'Vector,Vector':
>=(e1, e2)
## S3 method for class 'Vector,ANY':
>=(e1, e2)
## S3 method for class 'ANY,Vector':
>=(e1, e2)
## S3 method for class 'Vector,Vector':
<(e1, e2)="" ##="" s3="" method="" for="" class="" 'vector,any':="" <(e1,="" 'any,vector':="" e2)<="" p="">
## S3 method for class 'Vector,Vector':
>(e1, e2)
## S3 method for class 'Vector,ANY':
>(e1, e2)
## S3 method for class 'ANY,Vector':
>(e1, e2)
## selfmatch()
## -----------
selfmatch(x, ...)
## duplicated() & unique()
## -----------------------
## S3 method for class 'Vector':
duplicated(x, incomparables=FALSE, ...)
## S3 method for class 'Vector':
unique(x, incomparables=FALSE, ...)
#### ----
## S3 method for class 'Vector,Vector':
%in%(x, table)
## S3 method for class 'Vector,ANY':
%in%(x, table)
## S3 method for class 'ANY,Vector':
%in%(x, table)
## findMatches() & countMatches()
## ------------------------------
findMatches(x, table, select=c("all", "first", "last"), ...)
countMatches(x, table, ...)
## sort()
## ------
## S3 method for class 'Vector':
sort(x, decreasing=FALSE, na.last = NA, by)
## table()
## -------
## S3 method for class 'Vector':
table(...)

Arguments

x, y, e1, e2, table

Vector-like objects.

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.

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.

decreasing, na.last

See ?base::sort.

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 defaultselfmatchmethod, which is implemented on top ofmatch, propagates the extra arguments to its call tomatch.
Theduplicatedmethod forVectorobjects, which is implemented on top ofselfmatch, accepts extra argumentfromLastand propagates the other extra arguments to its call toselfmatch. See?base::duplicatedfor more information about this argument.
Theuniquemethod forVectorobjects, which is implemented on top ofduplicated, propagates the extra arguments to its call toduplicated.
The defaultfindMatchesandcountMatchesmethods, which are implemented on top ofmatchandselfmatch, propagate the extra arguments to their calls tomatchandselfmatch.
Thesortmethod forVectorobjects, which is implemented on top oforder, only accepts extra argumentna.lastand propagates it to its call toorder.

Value

For pcompare: see Details section above.
For 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 table: a 1D array of integer values promoted to the "table" class. See ?BiocGeneric::table for more information.

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 method is implemented. However note that selfmatch(x, ...) will typically be more efficient than match(x, x, ...) on vector-like objects for which a specific selfmatch method is implemented.

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.

Examples

Run this code

## ---------------------------------------------------------------------
## 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 ?`Ranges-comparison` for more examples (on Ranges 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(".-+"))))

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