Given two sets of gene lists, this package calculates the overlaps between all pairs of lists from the two sets. Fisher's exact test is used to determine the p-value and odds ratio in comparison to a genomic background. Plotting functions are provided to visualize the results.
To use the package, construct one or two named lists each representing a gene set. Each list should contain one or more vectors of gene names. Then use GeneOverlapMatrix to perform pairwise comparisons. It will return an object that can be used for visualization. The GeneOverlapMatrix calls GeneOverlap internally to perform comparison between two gene lists.
Li Shen <firstname.lastname@example.org>
Mount Sinai profile:http://www.mountsinai.org/profiles/li-shen
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