1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
|
\name{order}
\alias{order}
\title{Ordering permutation}
\description{
\code{order} returns a permutation which rearranges its first argument
into ascending or descending order, breaking ties by further
arguments.
NOTE: This man page is for the \code{order} \emph{S4 generic function}
defined in the \pkg{BiocGenerics} package.
See \code{?base::\link[base]{order}} for the default method
(defined in the \pkg{base} package).
Bioconductor packages can define specific methods for objects
(typically vector-like) not supported by the default method.
}
\usage{
order(..., na.last=TRUE, decreasing=FALSE)
}
\arguments{
\item{...}{
One or more vector-like objects, all of the same length.
}
\item{na.last, decreasing}{
See \code{?base::\link[base]{order}} for a description of
these arguments.
}
}
\value{
The default method (see \code{?base::\link[base]{order}}) returns
an integer vector of length N where N is the common length of the
input objects. This integer vector represents a permutation of N
elements and can be used to rearrange the first argument in
\code{...} into ascending or descending order (by subsetting it).
Specific methods defined in Bioconductor packages should also
return an integer vector representing a permutation of N elements.
}
\note{
TO DEVELOPPERS:
Specific \code{order} methods should preferably be made "stable" for
consistent behavior across platforms and consistency with
\code{base::order()}. Note that C qsort() is \emph{not} "stable" so
\code{order} methods that use qsort() at the C-level need to ultimately
break ties by position, which can easily be done by adding a little
extra code at the end of the comparison function passed to qsort().
\code{order(x, decreasing=TRUE)} is \emph{not} always equivalent to
\code{rev(order(x))}.
\code{\link[BiocGenerics]{order}}, \code{\link[BiocGenerics]{sort}},
and \code{\link[BiocGenerics]{rank}} methods for specific vector-like
objects should adhere to the same underlying order that should be
conceptually defined as a binary relation on the set of all possible
vector values. For completeness, this binary relation should also be
incarnated by a \link{<=} method.
}
\seealso{
\itemize{
\item \code{base::\link[base]{order}} for the default \code{order} method.
\item \code{\link[methods]{showMethods}} for displaying a summary of the
methods defined for a given generic function.
\item \code{\link[methods]{selectMethod}} for getting the definition of
a specific method.
\item \link[IRanges]{order,Ranges-method} in the \pkg{IRanges} package
for an example of a specific \code{order} method (defined for
\link[IRanges]{Ranges} objects).
\item \link{BiocGenerics} for a summary of all the generics defined
in the \pkg{BiocGenerics} package.
}
}
\examples{
order
showMethods("order")
selectMethod("order", "ANY") # the default method
}
\keyword{methods}
|