SummarizedBenchmark-class {SummarizedBenchmark} | R Documentation

## SummarizedBenchmark class

### Description

Extension of the `RangedSummarizedExperiment` to store the output of different methods intended for the same purpose in a given dataset. For example, a differential expression analysis could be done using limma-voom, edgeR and DESeq2. The SummarizedBenchmark class provides a framework that is useful to store, benckmark and compare results.

### Slots

`performanceMetrics`

  A `SimpleList` of the same length as the number of `assays` containing performance functions to be compared with the ground truths.

`BenchDesign`

  A `BenchDesign` originally used to generate the results in the object.

### Author(s)

Alejandro Reyes

### Examples

    ## loading the example data from iCOBRA
    library(iCOBRA)
    data(cobradata_example)

    ## a bit of data wrangling and reformatting
    assays <- list(
        qvalue=cobradata_example@padj,
        logFC=cobradata_example@score )
    assays[["qvalue"]]$DESeq2 <- p.adjust(cobradata_example@pval$DESeq2, method="BH")
    groundTruth <- DataFrame( cobradata_example@truth[,c("status", "logFC")] )
    colnames(groundTruth) <- names( assays )
    colData <- DataFrame( method=colnames(assays[[1]]) )
    groundTruth <- groundTruth[rownames(assays[[1]]),]

    ## constructing a SummarizedBenchmark object
    sb <- SummarizedBenchmark(
        assays=assays, colData=colData,
        groundTruth=groundTruth )

[Package SummarizedBenchmark version 2.5.0 Index]