Pathway analysis aims to provide insight into the biological processes involved by aggregating the association signal observed for a collection of SNPs into a pathway level signal. This is generally carried out in two steps: first, individual SNPs are mapped to genes and their association p-values are combined into gene scores; second, genes are grouped into pathways and their gene scores are combined into pathway scores. Existing tools vary in the methods used for each step and the strategies employed to correct for correlation due to linkage disequilibrium.
