enrichment_test: perform enrichment testing using topGO and fisher's exact...

In tmirus/TTT: What the Package Does (One Line, Title Case)

Description

perform enrichment testing using topGO and fisher's exact test for a given gene list

Usage

enrichment_test(
  all.genes,
  genelist,
  db,
  go_ids = NULL,
  sig.level = 0.05,
  max.terms = 5000,
  node.size = 10
)

Arguments

all.genes	character vector, the reference gene set. for example all genes in the experiment
genelist	character vector, list of interesting genes
db	biomaRt database for the data
go_ids	table assigning GO ids to gene names, obtained using getBM
sig.level	numeric, 0 < sig.level < 1. Significance cutoff, p-values above this threshold are discarded
max.terms	numeric > 0, maximum number of terms to be considered
node.size	ignore GO nodes with less than node.size annotated genes

Value

table containing information about each significant GO term

tmirus/TTT documentation built on April 17, 2021, 11:04 p.m.