getMset: getMset method

In biosigner: Signature discovery from omics data

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)

biosigner documentation built on Nov. 24, 2020, 2 a.m.