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

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: Obtain the specified assay with a numberic or character reference

• assays: Get the assay data from each element in the ExperimentList

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()