chain.fisher.enrich: chain.fisher()

In PNNL-Comp-Mass-Spec/Rodin: Lipid Mini-on

chain.fisher()

Description

Provide a rapid way to perform fisher.tests on <.allchains> objects created using the lipid.miner function.

Usage

chain.fisher.enrich(X, Y, pval = 0.05, adjpval = 1)

Arguments

X	any <Query.allchains> object
Y	any <Universe.allchains> object
pval	is a regular pvalue to use as a cutoff for the enrichment
adjpval	is a BH adjusted pvalue to use as a cutoff for the enrichment

Details

The difference between the chain.fisher and the chain.fisher.enrich function is that the <.enrich> function allows to extract only the element that are enriched according to a Pvalue or a BH adjusted pvalue.

the universe file db.allchains is provided if you are lacking an universe file

Value

This function will return a data frame with the results of the tests

Author(s)

Geremy Clair

Examples

chain.fisher.enrich(queryExample.chain, universeExample.chain)

PNNL-Comp-Mass-Spec/Rodin documentation built on Jan. 28, 2024, 2:12 a.m.