Random gene enrichment

Gene Score Resampling assesses the significance of gene scores annotated to a specific GO category relative to a null model in which scores are assigned to genes at random. This method for gene category enrichment is implemented in the function SingleEnrichment.

INPUTS:

• geneScores, a numGenes-long column vector of values that quantifies something about each gene.
• geneEntrezIDs, numGenes-long column vector labeling the entrez ID for each gene in geneScores. Extra options set as fields in the parameter structure, enrichmentSettings.

EXAMPLE USAGE:

enrichmentSettings = GiveMeDefaultEnrichmentParams();
GOTable = SingleEnrichment(geneScores,geneEntrezIDs,enrichmentSettings);

The output GOTable sorts GO categories by their estimated p-value. Note that p-values are estimated according to two different methods:

1. pValPerm: p-value from a permutation test.
2. pValZ: p-value estimated from a Gaussian fit to the null distribution.

Both p-value estimates are corrected using the method of false discovery rate (Benjamini and Hochberg), in the corresponding columns pValPermCorr and pValZCorr.