test.overrepresentation {gene2pathway} | R Documentation |
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.
test.overrepresentation(genesOfInterest, predpath, KEGGonly=FALSE, cutoff=0.1, min.conf=0.9, adj.method="BY")
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 |
Table with two columns: KEGG pathway and adjusted p-value (adjustment according to Benjamini-Yekutieli)