fgseaPostprocessing {NanoTube} | R Documentation

## Postprocessing for GSEA analyses

### Description

Clusters GSEA results by leading edge genes, and writes reports showing gene expression profiles of these genes.

### Usage

    fgseaPostprocessing(
      genesetResults,
      leadingEdge,
      limmaResults,
      join.threshold = 0.5,
      ngroups = NULL,
      dist.method = "binary",
      reportDir
    )

### Arguments

`genesetResults` | Results from pathway analysis using limmaToFGSEA.
`leadingEdge` | Results from fgseaToLEdge
`limmaResults` | Results from runLimmaAnalysis
`join.threshold` | The threshold distance to join gene sets. Gene sets with a distance below this value will be joined to a single "cluster."
`ngroups` | The desired number of gene set groups. Either 'join.threshold' or 'ngroups' must be specified, 'ngroups' takes priority if both are specified.
`dist.method` | Method for distance calculation (see options for dist()). We recommend the 'binary' (also known as Jaccard) distance.
`reportDir` | Directory for the GSEA reports (each comparison will be a separate txt file). Directory will be created if it does not exist.

### Value

A table of gene set analysis results, as well as reports showing differential expression of leading edge genes.

### Examples

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

    fgseaResults <- limmaToFGSEA(ExampleResults, gene.sets = ExamplePathways)

    leadingEdge <- fgseaToLEdge(fgseaResults, cutoff.type = "padj", cutoff = 0.1)

    fgseaPostprocessing(fgseaResults, leadingEdge,
                        limmaResults = ExampleResults,
                        join.threshold = 0.5,
                        reportDir = "GSEAresults")

[Package NanoTube version 1.0.0 Index]