The gene-set analysis is divided into two distinct and largely independent parts. In the first part a gene analysis is performed to quantify the degree of association each gene has with the phenotype. In addition the correlations between genes are estimated. These correlations reflect the LD between genes, and are needed in order to compensate for the dependencies between genes during the gene-set analysis. The gene p-values and gene correlation matrix are then used in the second part to perform the actual gene-set analysis.
