getMset {ropls} | R Documentation |
Extracts the complemented MultiDataSet when opls has been applied to a MultiDataSet
getMset(object, ...) ## S4 method for signature 'oplsMultiDataSet' getMset(object)
object |
An S4 object of class |
... |
Currently not used |
An S4 object of class MultiDataSet
.
# 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)