ExperimentList-class {MultiAssayExperiment}R Documentation

ExperimentList - A container for multi-experiment data The ExperimentList class is a container that builds on the SimpleList with additional checks for consistency in experiment names and length. It contains a SimpleList of experiments with sample identifiers. One element present per experiment performed. Convert from SimpleList or list to the multi-experiment data container. When using the mergeReplicates method, additional arguments are passed to the given simplify function argument (e.g., na.rm = TRUE)

Description

ExperimentList - A container for multi-experiment data

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

Convert from SimpleList or list to the multi-experiment data container. When using the mergeReplicates method, additional arguments are passed to the given simplify function argument (e.g., na.rm = TRUE)

Usage

## S4 method for signature 'ExperimentList'
show(object)

## S4 method for signature 'ExperimentList'
isEmpty(x)

## S4 method for signature 'ExperimentList'
dimnames(x)

## S4 method for signature 'ExperimentList'
mergeReplicates(x, replicates = list(), simplify = BiocGenerics::mean, ...)

## S4 method for signature 'ANY,missing'
assay(x, i, withDimnames = TRUE, ...)

## S4 method for signature 'ExperimentList'
assays(x, withDimnames = TRUE, ...)

## S4 method for signature 'ExperimentList,missing'
assay(x, i, withDimnames = TRUE, ...)

## S4 method for signature 'ExperimentList,numeric'
assay(x, i, withDimnames = TRUE, ...)

## S4 method for signature 'ExperimentList,character'
assay(x, i, withDimnames = TRUE, ...)

Arguments

object, x

An ExperimentList object

replicates

mergeReplicates: A list or LogicalList where each element represents a sample and a vector of repeated measurements for the sample

simplify

A function for merging columns where duplicates are indicated by replicates

...

Additional arguments. See details for more information.

i

A scalar character or integer index

withDimnames

logical (default TRUE) whether to return dimension names

Value

An ExperimentList class object

Methods (by generic)

coercion

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

In the following example, x is either a list or List:

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

Examples


ExperimentList()


[Package MultiAssayExperiment version 1.18.0 Index]