aucScores-class {RcisTarget} | R Documentation

## Class to store the AUC scores for RcisTarget.

### Description

Contains the AUC scores for each gene- or region-set. They can be accessed through `getAUC()` and the regular methods (i.e. nrow, rownames... ) available for SummarizedExperiment objects.

### Usage

    ## S4 method for signature 'aucScores'
    show(object)

    ## S4 method for signature 'aucScores'
    getAUC(object)

### Arguments

`object` | Results from `calcAUC`.

### Value

- show: Prints a summary of the object

- getAUC: Returns the matrix containing the AUC scores

### Examples

    ##################################################
    # Setup & previous steps in the workflow:

    #### Gene sets
    # As example, the package includes an Hypoxia gene set:
    txtFile <- paste(file.path(system.file('examples', package='RcisTarget')),
                     "hypoxiaGeneSet.txt", sep="/")
    geneLists <- list(hypoxia=read.table(txtFile, stringsAsFactors=FALSE)[,1])

    #### Databases
    ## Motif rankings: Select according to organism and distance around TSS
    ## (See the vignette for URLs to download)
    # motifRankings <- importRankings("hg19-500bp-upstream-7species.mc9nr.feather")

    ## For this example we will use a SUBSET of the ranking/motif databases:
    library(RcisTarget.hg19.motifDBs.cisbpOnly.500bp)
    data(hg19_500bpUpstream_motifRanking_cispbOnly)
    motifRankings <- hg19_500bpUpstream_motifRanking_cispbOnly

    ## Motif - TF annotation:
    data(motifAnnotations_hgnc) # human TFs (for motif collection 9)
    motifAnnotation <- motifAnnotations_hgnc

    ### Run RcisTarget
    # Step 1. Calculate AUC
    motifs_AUC <- calcAUC(geneLists, motifRankings)

    ##################################################

    #Exploring the output:
    motifs_AUC

    class(motifs_AUC)

    # Extracting the AUC matrix:
    getAUC(motifs_AUC)[,1:5]

    # Subsetting and regular manipulation methods are also available:
    motifs_AUC[1,]
    motifs_AUC[,3:4]

    dim(motifs_AUC)
    nrow(motifs_AUC)
    ncol(motifs_AUC)
    colnames(motifs_AUC)
    rownames(motifs_AUC)

[Package RcisTarget version 1.0.2 Index]