getMset {ropls} | R Documentation

## getMset method

### Description

Extracts the complemented MultiDataSet when opls has been applied to a MultiDataSet

### Usage

    getMset(object, ...)

    ## S4 method for signature 'oplsMultiDataSet'
    getMset(object)

### Arguments

`object` | An S4 object of class `oplsMultiDataSet`, created by `opls` function applied to a MultiDataSet
`...` | Currently not used

### Value

An S4 object of class `MultiDataSet`.

### Examples

    # Building a MultiDataSet object
    # Loading the 'NCI60_4arrays' from the 'omicade4' package
    data("NCI60_4arrays", package = "omicade4")
    # Selecting two of the four datasets
    setNamesVc <- c("agilent", "hgu95")
    # Creating the MultiDataSet instance
    nciMset <- MultiDataSet::createMultiDataSet()
    # Adding the two datasets as ExpressionSet instances
    for (setC in setNamesVc) {
      # Getting the data
      exprMN <- as.matrix(NCI60_4arrays[[setC]])
      pdataDF <- data.frame(row.names = colnames(exprMN),
                            cancer = substr(colnames(exprMN), 1, 2),
                            stringsAsFactors = FALSE)
      fdataDF <- data.frame(row.names = rownames(exprMN),
                            name = rownames(exprMN),
                            stringsAsFactors = FALSE)
      # Building the ExpressionSet
      eset <- Biobase::ExpressionSet(assayData = exprMN,
                                     phenoData = new("AnnotatedDataFrame",
                                                     data = pdataDF),
                                     featureData = new("AnnotatedDataFrame",
                                                       data = fdataDF),
                                     experimentData = new("MIAME",
                                                          title = setC))
      # Adding to the MultiDataSet
      nciMset <- MultiDataSet::add_eset(nciMset, eset, dataset.type = setC,
                                        GRanges = NA, warnings = FALSE)
    }
    # Summary of the MultiDataSet
    nciMset
    # Principal Component Analysis of each data set
    nciPca <- ropls::opls(nciMset)
    # Getting the MultiDataSet with additional info. in pData and fData
    nciMset <- ropls::getMset(nciPca)

[Package ropls version 1.18.8 Index]