File: ExperimentList-class.Rd

package info (click to toggle)
r-bioc-multiassayexperiment 1.16.0%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: bookworm, bullseye
  • size: 924 kB
  • sloc: sh: 13; makefile: 2
file content (120 lines) | stat: -rw-r--r-- 3,957 bytes parent folder | download | duplicates (2)
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
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ExperimentList-class.R,
%   R/MultiAssayExperiment-methods.R, R/MultiAssayExperiment-helpers.R,
%   R/assay-methods.R
\docType{class}
\name{ExperimentList-class}
\alias{ExperimentList-class}
\alias{show,ExperimentList-method}
\alias{coerce-ExperimentList}
\alias{coerce,list,ExperimentList-method}
\alias{coerce,List,ExperimentList-method}
\alias{isEmpty,ExperimentList-method}
\alias{dimnames,ExperimentList-method}
\alias{mergeReplicates,ExperimentList-method}
\alias{assay,ANY,missing-method}
\alias{assays,ExperimentList-method}
\alias{assay,ExperimentList,missing-method}
\alias{assay,ExperimentList,numeric-method}
\alias{assay,ExperimentList,character-method}
\title{ExperimentList - A container for multi-experiment data

The \code{ExperimentList} class is a container that builds on
the \code{SimpleList} with additional
checks for consistency in experiment names and length.
It contains a \code{SimpleList} of experiments with sample identifiers.
One element present per experiment performed.

Convert from \code{SimpleList} or \code{list}
to the multi-experiment data container. When using the
\strong{mergeReplicates} method, additional arguments are passed to the
given \code{simplify} function argument (e.g., na.rm = TRUE)}
\usage{
\S4method{show}{ExperimentList}(object)

\S4method{isEmpty}{ExperimentList}(x)

\S4method{dimnames}{ExperimentList}(x)

\S4method{mergeReplicates}{ExperimentList}(x, replicates = list(), simplify = BiocGenerics::mean, ...)

\S4method{assay}{ANY,missing}(x, i, withDimnames = TRUE, ...)

\S4method{assays}{ExperimentList}(x, withDimnames = TRUE, ...)

\S4method{assay}{ExperimentList,missing}(x, i, withDimnames = TRUE, ...)

\S4method{assay}{ExperimentList,numeric}(x, i, withDimnames = TRUE, ...)

\S4method{assay}{ExperimentList,character}(x, i, withDimnames = TRUE, ...)
}
\arguments{
\item{object, x}{An \code{\linkS4class{ExperimentList}} object}

\item{replicates}{mergeReplicates: A \code{list} or \linkS4class{LogicalList}
where each element represents a sample and a vector of repeated measurements
for the sample}

\item{simplify}{A function for merging columns where duplicates are indicated
by replicates}

\item{...}{Additional arguments. See details for more information.}

\item{i}{A scalar \code{character} or \code{integer} index}

\item{withDimnames}{logical (default TRUE) whether to return dimension names}
}
\value{
An \code{ExperimentList} class object
}
\description{
ExperimentList - A container for multi-experiment data

The \code{ExperimentList} class is a container that builds on
the \code{SimpleList} with additional
checks for consistency in experiment names and length.
It contains a \code{SimpleList} of experiments with sample identifiers.
One element present per experiment performed.

Convert from \code{SimpleList} or \code{list}
to the multi-experiment data container. When using the
\strong{mergeReplicates} method, additional arguments are passed to the
given \code{simplify} function argument (e.g., na.rm = TRUE)
}
\section{Methods (by generic)}{
\itemize{
\item \code{show}: Show method for
\code{\linkS4class{ExperimentList}} class

\item \code{isEmpty}: check for zero length across all
experiments

\item \code{dimnames}: Get the dimension names for
an \code{ExperimentList} using \code{\linkS4class{CharacterList}}

\item \code{mergeReplicates}: Apply the mergeReplicates method on the
ExperimentList elements

\item \code{assay}: Obtain the specified assay with a \code{numeric}
or \code{character} reference

\item \code{assays}: Get the assay data from each element in the
\link{ExperimentList}
}}

\section{coercion}{

Convert a \code{list} or S4 \code{List} to an ExperimentList using the
\code{as()} function.

In the following example, \code{x} is either a \code{list} or
\linkS4class{List}:

\preformatted{    \code{as(x, "ExperimentList")}}
}

\examples{

ExperimentList()

}