File: SparseArraySeed-utils.Rd

package info (click to toggle)
r-bioc-delayedarray 0.24.0%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: bookworm
  • size: 1,480 kB
  • sloc: ansic: 727; makefile: 2
file content (137 lines) | stat: -rw-r--r-- 3,338 bytes parent folder | download
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
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
\name{SparseArraySeed-utils}

\alias{SparseArraySeed-utils}

\alias{rbind,SparseArraySeed-method}
\alias{cbind,SparseArraySeed-method}

\alias{is.na,SparseArraySeed-method}
\alias{is.infinite,SparseArraySeed-method}
\alias{is.nan,SparseArraySeed-method}
\alias{tolower,SparseArraySeed-method}
\alias{toupper,SparseArraySeed-method}
\alias{nchar,SparseArraySeed-method}

\alias{anyNA,SparseArraySeed-method}
\alias{which,SparseArraySeed-method}

\alias{max,SparseArraySeed-method}
\alias{min,SparseArraySeed-method}
\alias{range.SparseArraySeed}
\alias{range,SparseArraySeed-method}
\alias{sum,SparseArraySeed-method}
\alias{prod,SparseArraySeed-method}
\alias{any,SparseArraySeed-method}
\alias{all,SparseArraySeed-method}

\alias{mean.SparseArraySeed}
\alias{mean,SparseArraySeed-method}

\title{Operate natively on SparseArraySeed objects}

\description{
   Some utilities to operate natively on \link{SparseArraySeed} objects.
   Mostly for internal use by the \pkg{DelayedArray} package e.g. they
   support block processed methods for sparse \link{DelayedArray} objects
   like \code{sum()}, \code{mean()}, \code{which()}, etc...
}

\usage{
\S4method{is.na}{SparseArraySeed}(x)

\S4method{is.infinite}{SparseArraySeed}(x)

\S4method{is.nan}{SparseArraySeed}(x)

\S4method{tolower}{SparseArraySeed}(x)

\S4method{toupper}{SparseArraySeed}(x)

\S4method{nchar}{SparseArraySeed}(x, type="chars", allowNA=FALSE, keepNA=NA)

\S4method{anyNA}{SparseArraySeed}(x, recursive=FALSE)

\S4method{which}{SparseArraySeed}(x, arr.ind=FALSE, useNames=TRUE)


## <>-<>-<> "Summary" group generic <>-<>-<>

\S4method{max}{SparseArraySeed}(x, ..., na.rm=FALSE)

\S4method{min}{SparseArraySeed}(x, ..., na.rm=FALSE)

\S4method{range}{SparseArraySeed}(x, ..., finite=FALSE, na.rm=FALSE)

\S4method{sum}{SparseArraySeed}(x, ..., na.rm=FALSE)

\S4method{prod}{SparseArraySeed}(x, ..., na.rm=FALSE)

\S4method{any}{SparseArraySeed}(x, ..., na.rm=FALSE)

\S4method{all}{SparseArraySeed}(x, ..., na.rm=FALSE)


## <>-<>-<> others <>-<>-<>

\S4method{mean}{SparseArraySeed}(x, na.rm=FALSE)
}

\arguments{
  \item{x}{
    A \link{SparseArraySeed} object.
  }
  \item{type, allowNA, keepNA}{
    See \code{?base::\link[base]{nchar}} for a description of
    these arguments.
  }
  \item{recursive}{
    See \code{?base::\link[base]{anyNA}} for a description of
    this argument.
  }
  \item{arr.ind}{
    See \code{?base::\link[base]{which}} for a description of
    this argument.
  }
  \item{useNames}{
    Ignored.
  }
  \item{...}{
    Unsupported.
  }
  \item{na.rm}{
    \code{TRUE} or \code{FALSE} (the default).
    Should \code{NA}'s and \code{NaN}'s be removed?
  }
  \item{finite}{
    \code{TRUE} or \code{FALSE} (the default).
    Should non-finite values be removed?
  }
}

\value{
  See corresponding functions in the \pkg{base} package.
}

\seealso{
  \itemize{
    \item \link{SparseArraySeed} objects.
  }
}

\examples{
## Create a SparseArraySeed object:
dim1 <- 5:3
nzindex1 <- Lindex2Mindex(sample(60, 14), 5:3)
sas1 <- SparseArraySeed(dim1, nzindex1, nzdata=sample(0:13))

## Apply native operations:
sum(sas1)
range(sas1)
mean(sas1)

## Sanity checks:
stopifnot(identical(sum(as.array(sas1)), sum(sas1)))
stopifnot(identical(range(as.array(sas1)), range(sas1)))
stopifnot(identical(mean(as.array(sas1)), mean(sas1)))
}
\keyword{methods}