Functional enrichments

Source: R/enricher.R

Functional enrichments by hypergeometric test

enricher(
  test_gene_sets,
  ref_gene_sets,
  universe = NULL,
  minGSSize = 10,
  maxGSSize = 500,
  pAdjustMethod = "BH",
  pvalueCutoff = 0.05,
  qvalueCutoff = 0.2
)

Arguments

test_gene_sets

(list of) character vector gene IDs

ref_gene_sets

(list of) character vector gene IDs

universe

all genes considered. If NULL, uses all genes in test_gene_sets. Default: NULL

minGSSize

minimum gene set size, Default: 10

maxGSSize

maximum gene set size, Default: 500

pAdjustMethod

p-value adjustment method, Default: 'BH'

pvalueCutoff

p-value cutoff, Default: 0.05

qvalueCutoff

FDR cutoff, Default: 0.2

Value

dataframe with enrichment statistics.

Details

enriched ref_gene_sets per test_gene_set are returned. test_gene_set names are specified in the name column and ref_gene_set name are specified in the ID column.

Examples

if (FALSE) {
if(interactive()){
 #EXAMPLE1
 }
}