enricher: Functional enrichments

In jlaffy/scalop: Single Cell Analysis Operations

Functional enrichments

Description

Functional enrichments by hypergeometric test

Usage

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

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.

Value

dataframe with enrichment statistics.

See Also

alias2Symbol enricher

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

jlaffy/scalop documentation built on March 24, 2024, 9 a.m.