groupedGSEAtoStackedReport {NanoTube} | R Documentation

## Build a report from gene set enrichment results.

### Description

After clustering FGSEA results by gene set similarity, this function builds a report containing the individual gene expression profiles for genes contained in each gene set cluster.

### Usage

    groupedGSEAtoStackedReport(grouped.gsea, leadingEdge, de.fit, outputDir = NULL)

### Arguments

`grouped.gsea` | Output from groupFGSEA()
`leadingEdge` | Leading edge analysis results used in groupFGSEA()
`de.fit` | Differential Expression results from Limma or NanoStringDiff
`outputDir` | Directory for output files. If NULL (default), will return the stacked report instead of writing to a file.

### Value

A stacked report containing statistics and gene expression profiles for genes contained in each cluster

### Examples

    data("ExamplePathways")
    data("ExampleResults") # Results from runLimmaAnalysis

    fgseaResults <- limmaToFGSEA(ExampleResults, gene.sets = ExamplePathways,
                                 min.set = 5, rank.by = "t")
    leadingEdge <- fgseaToLEdge(fgseaResults, cutoff.type = "padj", cutoff = 0.1)

    fgseaGrouped <- groupFGSEA(fgseaResults$Autoimmune.retinopathy,
                                leadingEdge$Autoimmune.retinopathy,
                                join.threshold = 0.5,
                                dist.method = "binary")

    results.AR <- groupedGSEAtoStackedReport(
                  fgseaGrouped,
                  leadingEdge = leadingEdge$Autoimmune.retinopathy,
                  de.fit = ExampleResults)

[Package NanoTube version 1.0.0 Index]