Simple overrepresentation analysis based on hypergeometric test
Simple overrepresentation analysis based on hypergeometric test
fora(pathways, genes, universe, minSize = 1, maxSize = Inf)
pathways |
List of gene sets to check. |
genes |
Set of query genes |
universe |
A universe from whiche 'genes' were selected |
minSize |
Minimal size of a gene set to test. All pathways below the threshold are excluded. |
maxSize |
Maximal size of a gene set to test. All pathways above the threshold are excluded. |
A table with ORA results. Each row corresponds to a tested pathway. The columns are the following:
pathway – name of the pathway as in 'names(pathway)';
pval – an enrichment p-value from hypergeometric test;
padj – a BH-adjusted p-value;
overlap – size of the overlap;
size – size of the gene set;
leadingEdge – vector with overlapping genes.
data(examplePathways) data(exampleRanks) foraRes <- fora(examplePathways, genes=tail(names(exampleRanks), 200), universe=names(exampleRanks))
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