test.overrepresentation {gene2pathway}R Documentation

Test statistical overrepresentation of KEGG pathways in a list of genes

Description

Test the statistical overrepresentation of KEGG pathways in a group of genes using Fisher's exact test. The analysis can either be based on all KEGG pathways predicted by gene2pathway/gene2pathway.signaltrans or on original KEGG annotation only.

Usage

test.overrepresentation(genesOfInterest, predpath, KEGGonly=FALSE, cutoff=0.1, min.conf=0.9, adj.method="BY")

Arguments

genesOfInterest a character vector of gene identifiers (see gene2pathway, gene2pathway.signaltrans) for a gene list of interest
predpath predictions of gene2pathway or gene2pathway.signaltrans
KEGGonly use KEGG annotation only
cutoff p-value significance cutoff
min.conf filter predictions such that only those with a confidence score > min.conf are considered
adj.method multiple testing correction method. Default: Benjamini-Yekutieli

Value

Table with two columns: KEGG pathway and adjusted p-value (adjustment according to Benjamini-Yekutieli)


[Package gene2pathway version 1.2.0 Index]