Iuliana-Ionita-Laza/GeneScan3DKnock: Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes

Functions for the gene-based association tests that integrate both common and rare genetic variation from promoter and enhancers for each gene, along with the knockoff-enhanced tests. The GeneScan3DKnock has two steps: Step 1. Knockoff generation using function GeneScan3D.KnockoffGeneration() and Step 2. Knockoff filter using function GeneScan3DKnock(). To deal with case-control imbalance issue for binary traits, we apply the Saddlepoint approximation (SPA) of the gene-based tests to avoid the inflation of Type I error rate. The knockoff generations are optimized using shrinkage leveraging algorithm.

install.packages("remotes")
remotes::install_github("Iuliana-Ionita-Laza/GeneScan3DKnock")