aucellResults-class {AUCell} | R Documentation |
This class extends SummarizedExperiment to contain the AUC matrix and cell rankings (as 'assays').
The results are stored in the assays slot, but they can be accessed through the regular methods (i.e. nrow, rownames... )
Types:
- "AUC": The assays contains the AUC for the gene-sets (or region-sets) & cells.
- "ranking": The assays contains the gene rankings for each cell.
## S4 method for signature 'aucellResults' show(object) getAUC(object) ## S4 method for signature 'aucellResults' getAUC(object) getRanking(object) ## S4 method for signature 'aucellResults' getRanking(object)
object |
Results from |
show: Prints a summary of the object
getAUC: Returns the matrix containing the AUC
getRanking: Returns the matrix containing the rankings
# This example is run using a fake expression matrix. # Therefore, the output will be meaningless. ############# Fake run of AUCell ############# set.seed(123) exprMatrix <- matrix(data=sample(c(rep(0, 5000), sample(1:3, 5000, replace=TRUE))), nrow=20, dimnames=list(paste("Gene", 1:20, sep=""), paste("Cell", 1:500, sep=""))) dim(exprMatrix) # Running AUCell cells_rankings <- AUCell_buildRankings(exprMatrix) fewGenes <- sample(rownames(exprMatrix), 10) otherGenes <- sample(rownames(exprMatrix), 5) geneSets <- list(geneSet1=fewGenes, geneSet2=otherGenes) cells_AUC <- AUCell_calcAUC(geneSets, cells_rankings, aucMaxRank=5, nCores=1) ############################################## #Exploring the output: cells_AUC class(cells_AUC) # Extracting the AUC matrix: getAUC(cells_AUC)[,1:5] # Subsetting and regular manipulation methods are also available: cells_AUC[1:2,] cells_AUC[,3:4] dim(cells_AUC) nrow(cells_AUC) ncol(cells_AUC) colnames(cells_AUC) rownames(cells_AUC)