aucellResults-class {AUCell} | R Documentation

## Wrapper to the matrix that stores the AUC or the cell rankings.

### Description

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.

### Usage

    ## 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)

### Arguments

`object` | Results from `AUCell_buildRanking` or `AUCell_calcAUC`.

### Value

- show: Prints a summary of the object

- getAUC: Returns the matrix containing the AUC

- getRanking: Returns the matrix containing the rankings

### Examples

    # 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)

[Package AUCell version 1.6.1 Index]