fgseaToLEdge: Generate leading edge matrix from fgsea results.

In calebclass/NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

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)

calebclass/NanoTube documentation built on Nov. 21, 2023, 12:31 p.m.