Gene set enrichment analysis (GSEA) is typically based on tests derived from the Kolmogorov-Smirnov, which is underpowered and a need for simpler methods has been identified. The wgsea package contains functions for conducting GSEA using a Wilcoxon test to test for differences in the distribution of p values between SNPs within the gene set under test and a control set of SNPs.
See the vignette for further details.
Chris Wallace <email@example.com>
Irizarry, R. A.; Wang, C.; Zhou, Y. & Speed, T. P. Gene set enrichment analysis made simple. Stat Methods Med Res 2009, 18, 565-575
Heinig, M.; Petretto, E.; Wallace, C.; et al. A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk. Nature 2010, 467, 460-464