ExperimentList-class: ExperimentList - A container for multi-experiment data

In vjcitn/biocMultiAssay: Software for the integration of multi-omics experiments in Bioconductor

ExperimentList - 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.

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'
colnames(x, do.NULL = TRUE, prefix = "col")

## S4 method for signature 'ExperimentList'
rownames(x, do.NULL = TRUE, prefix = "row")

## 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
do.NULL, prefix	See ?base::rownames for a description of these arguments.
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)

• show(ExperimentList): Show method for ExperimentList class

• isEmpty(ExperimentList): check for zero length across all experiments

• dimnames(ExperimentList): Get the dimension names for an ExperimentList using CharacterList

• colnames(ExperimentList): Get the column names for an ExperimentList as a CharacterList slightly more efficiently

• rownames(ExperimentList): Get the row names for an ExperimentList as a CharacterList slightly more efficiently

• mergeReplicates(ExperimentList): Apply the mergeReplicates method on the ExperimentList elements

• assay(x = ANY, i = missing): Obtain the specified assay with a numeric or character reference

• assays(ExperimentList): 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()

vjcitn/biocMultiAssay documentation built on Feb. 7, 2024, 11:20 a.m.