ExperimentList {MultiAssayExperiment} | R Documentation

## Represent multiple experiments as a List-derivative `ExperimentList`

### Description

The `ExperimentList` class can contain several different types of data. The only requirements for an `ExperimentList` class are that the objects contained have the following set of methods: `dim`, `[`, `dimnames`

### Usage

    ExperimentList(...)

### Arguments

`...` | A named `list` class object

### Value

A `ExperimentList` class object of experiment data

### Examples

    ## Create an empty ExperimentList instance
    ExperimentList()

    ## Create array matrix and AnnotatedDataFrame to create an ExpressionSet class
    arraydat <- matrix(data = seq(101, length.out = 20), ncol = 4,
        dimnames = list(
            c("ENST00000294241", "ENST00000355076",
            "ENST00000383706","ENST00000234812", "ENST00000383323"),
            c("array1", "array2", "array3", "array4")
        ))

    colDat <- data.frame(slope53 = rnorm(4),
        row.names = c("array1", "array2", "array3", "array4"))

    ## SummarizedExperiment constructor
    exprdat <- SummarizedExperiment::SummarizedExperiment(arraydat,
        colData = colDat)

    ## Create a sample methylation dataset
    methyldat <- matrix(data = seq(1, length.out = 25), ncol = 5,
        dimnames = list(
            c("ENST00000355076", "ENST00000383706",
              "ENST00000383323", "ENST00000234812", "ENST00000294241"),
            c("methyl1", "methyl2", "methyl3",
              "methyl4", "methyl5")
        ))

    ## Create a sample RNASeqGene dataset
    rnadat <- matrix(
        data = sample(c(46851, 5, 19, 13, 2197, 507,
            84318, 126, 17, 21, 23979, 614), size = 20, replace = TRUE),
        ncol = 4,
        dimnames = list(
            c("XIST", "RPS4Y1", "KDM5D", "ENST00000383323", "ENST00000234812"),
            c("samparray1", "samparray2", "samparray3", "samparray4")
        ))

    ## Create a mock RangedSummarizedExperiment from a data.frame
    rangedat <- data.frame(chr="chr2", start = 11:15, end = 12:16,
        strand = c("+", "-", "+", "*", "."),
        samp0 = c(0,0,1,1,1), samp1 = c(1,0,1,0,1), samp2 = c(0,1,0,1,0),
        row.names = c(paste0("ENST", "00000", 135411:135414), "ENST00000383323"))

    rangeSE <- SummarizedExperiment::makeSummarizedExperimentFromDataFrame(rangedat)

    ## Combine to a named list and call the ExperimentList constructor function
    assayList <- list(Affy = exprdat, Methyl450k = methyldat, RNASeqGene = rnadat,
                    GISTIC = rangeSE)

    ## Use the ExperimentList constructor
    ExpList <- ExperimentList(assayList)

[Package MultiAssayExperiment version 1.20.0 Index]