getMset,biosignMultiDataSet-method {biosigner} | R Documentation

## getMset method

### Description

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

### Usage

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

### Arguments

`object` | An S4 object of class `biosignMultiDataSet`, created by `biosign` function applied to a MultiDataSet

### Value

An S4 object of class `MultiDataSet`.

### Examples

    # 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)
    }
    # Restricting to the 'ME' and 'LE' cancer types
    sampleNamesVc <- Biobase::sampleNames(nciMset[["agilent"]])
    cancerTypeVc <- Biobase::pData(nciMset[["agilent"]])[, "cancer"]
    nciMset <- nciMset[sampleNamesVc[cancerTypeVc %in% c("ME", "LE")], ]
    # Summary of the MultiDataSet
    nciMset
    # Selecting the significant features for PLS-DA, RF, and SVM classifiers, and getting back the updated MultiDataSet
    nciBiosign <- biosigner::biosign(nciMset, "cancer")
    nciMset <- biosigner::getMset(nciBiosign)
    # In the updated MultiDataSet, the updated featureData now contains the cancer_biosign_'classifier' columns
    # indicating the selected features
    lapply(fData(nciMset), head)

[Package biosigner version 1.20.0 Index]