getMset: getMset method

In ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data

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)

ropls documentation built on Nov. 8, 2020, 7:46 p.m.