ExperimentList-class {MultiAssayExperiment} | R Documentation

## A container for multi-experiment data

### Description

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.

### 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, ...)

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

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

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

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

### 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

### Details

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)

### Methods (by generic)

- `show`: Show method for `ExperimentList` class

- `isEmpty`: check for zero length across all experiments

- `dimnames`: Get the dimension names for an `ExperimentList` using `CharacterList`

- `mergeReplicates`: Apply the mergeReplicates method on the ExperimentList elements

- `assay`: Get the assay data for the default ANY class

- `assays`: Get the assay data from each element in the ExperimentList

- `assay`: Convenience function for the assay of the first element

- `assay`: Obtain the specified assay from ExperimentList with a `numeric` index

- `assay`: Get the specified assay from ExperimentList with a `character` index

### 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 1.6.0 Index]