enrichmentTestFisher: Enrichment with Fisher's Exact Test (Hypergeometric)

In sdgamboa/misctoolsr: What the Package Does (One Line, Title Case)

Enrichment with Fisher's Exact Test (Hypergeometric)

Description

enrichmentTestFisher performs a one-sided overrepresentation enrichment analysis using Fisher's exact test (hypergeometric). The function also calculates the odds.ratio using the epitools::oddsratio.wald function.

Usage

enrichmentTestFisher(contabs)

Arguments

contabs

A iist of contingency tables (xtabs objects); output from contingencyTable.

Value

A data frame; a report containing the p-value and odds ratio for each set x signature combination in the input list of contingency tables

See Also

contingencyTable; enrichmentTestFisher; ora

Other enrichment functions: contingencyTable(), ora()

Examples

library(misctoolsr)
se <- exampleSE()
sigs <- exampleSignatures()
contabs <- contingencyTable(x = se, cols = c("up", "down"), signatures = sigs)
contabs

enrichment_result <- enrichmentTestFisher(contabs)
enrichment_result

sdgamboa/misctoolsr documentation built on May 4, 2022, 12:33 p.m.