MultiAssayExperiment: Construct a 'MultiAssayExperiment' object

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

Description

The constructor function for the MultiAssayExperiment-class combines multiple data elements from the different hierarchies of data (study, experiments, and samples). It can create instances where neither a sampleMap or a colData set is provided. Please see the MultiAssayExperiment API documentation for more information by running the API function.

Usage

MultiAssayExperiment(experiments = ExperimentList(),
  colData = S4Vectors::DataFrame(), sampleMap = S4Vectors::DataFrame(assay =
  factor(), primary = character(), colname = character()), metadata = NULL,
  drops = list())

Arguments

experiments	A list or ExperimentList of all combined experiments
colData	A DataFrame or data.frame of characteristics for all biological units
sampleMap	A DataFrame or data.frame of assay names, sample identifiers, and colname samples
metadata	An optional argument of "ANY" class (usually list) for content describing the experiments
drops	A list of unmatched information (included after subsetting)

Value

A MultiAssayExperiment object that can store experiment and phenotype data

See Also

MultiAssayExperiment-class

Examples

## Run the example ExperimentList
example("ExperimentList")

## Create sample maps for each experiment
exprmap <- data.frame(
    primary = c("Jack", "Jill", "Barbara", "Bob"),
    colname = c("array1", "array2", "array3", "array4"),
    stringsAsFactors = FALSE)

methylmap <- data.frame(
    primary = c("Jack", "Jack", "Jill", "Barbara", "Bob"),
    colname = c("methyl1", "methyl2", "methyl3", "methyl4", "methyl5"),
    stringsAsFactors = FALSE)

rnamap <- data.frame(
    primary = c("Jack", "Jill", "Bob", "Barbara"),
    colname = c("samparray1", "samparray2", "samparray3", "samparray4"),
    stringsAsFactors = FALSE)

gistmap <- data.frame(
    primary = c("Jack", "Bob", "Jill"),
    colname = c("samp0", "samp1", "samp2"),
    stringsAsFactors = FALSE)

## Combine as a named list and convert to a DataFrame
mylist <- list(Affy = exprmap, Methyl450k = methylmap,
    RNASeqGene = rnamap, GISTIC = gistmap)

## Create a sampleMap
mySampleMap <- listToMap(mylist)
## Create an example phenotype data
colDat <- data.frame(sex = c("M", "F", "M", "F"), age = 38:41,
    row.names = c("Jack", "Jill", "Bob", "Barbara"))

## Create a MultiAssayExperiment instance
myMultiAssayExperiment <- MultiAssayExperiment(experiments = ExpList,
    colData = colDat, sampleMap = mySampleMap)

vjcitn/MultiAssayExperiment documentation built on May 3, 2019, 6:13 p.m.