fgseaToLEdge {NanoTube} | R Documentation

## Generate leading edge matrix from fgsea results.

### Description

Extract leading edge genes from gene sets identified in fgsea analysis. Gene sets may be filtered by significance or NES.

### Usage

    fgseaToLEdge(
      fgsea.res,
      cutoff.type = c("padj", "pval", "NES", "none"),
      cutoff = 0.05,
      nes.abs.cutoff = TRUE
    )

### Arguments

`fgsea.res` | Result from limmaToFGSEA
`cutoff.type` | Filter gene sets by adjusted p-value ('padj'), nominal p-value ('pval'), normalized enrichment score ('NES'), or include all gene sets ('none')
`cutoff` | Numeric cutoff for filtering (not used if cutoff.type == "none")
`nes.abs.cutoff` | If cutoff.type == "NES", should we use extreme positive and negative values (TRUE), or only filter in the positive or negative direction (FALSE). If TRUE, will select gene sets with abs(NES) > cutoff. If FALSE, will select gene sets with NES > cutoff (if cutoff >= 0) or NES < cutoff (if cutoff < 0)

### Value

a list containing the leading edge matrix for each comparison

### Examples

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

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

    # Generate the leading edge for pathways with padj < 0.25
    leadingEdge <- fgseaToLEdge(fgseaResults,
                                cutoff.type = "padj", cutoff = 0.25)

    # Generate the leading edge for pathways with abs(NES) > 2
    leadingEdge <- fgseaToLEdge(fgseaResults, cutoff.type = "NES",
                                cutoff = 2, nes.abs.cutoff = TRUE)

[Package NanoTube version 1.0.0 Index]