annotateModules-methods: Annotate Network Modules

In funnell/reactomefi: Reactome FI network analysis tools

Description

Perform gene set enrichment analysis on clustered network modules with pathways or GO terms.

Usage

annotateModules(object, type = c("Pathway", "BP", "CC", "MF"),
  min.module.size = 1, include.linkers = FALSE)

## S4 method for signature 'ReactomeFINetwork'
annotateModules(object, type = c("Pathway",
  "BP", "CC", "MF"), min.module.size = 1, include.linkers = FALSE)

Arguments

object	ReactomeFINetwork object.
type	Character string containing the type of annotation to use. Accepted values are "Pathway", "BP" for biological process, "CC" for cellular component, and "MF" for molecular function.
min.module.size	Minimum module size to consider for annotation (default: 1).
include.linkers	Set to TRUE if linker genes in the network should be included in network annotation. This may bias results. (default: FALSE)

Value

data.frame Results of the gene set enrichment analysis. The output will be the same as the annotate method plus another column for the module the annotation corresponds to.

funnell/reactomefi documentation built on May 16, 2019, 4:05 p.m.