ExperimentList: Represent multiple experiments as a List-derivative...

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

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)

vjcitn/biocMultiAssay documentation built on Dec. 24, 2024, 8:02 a.m.