PEPIS include four function modules: 1) kinship matrix calculation(km_calc), 2) poygenic component analysis(pg_anal), 3) genome scanning for main genetic effect(gs_main), 4) genome scanning for epistatic genetic effect(gs_epis).
PEPIS need the additive and dominance genotypic data files as the inputs to calculate the 6 polygenic kinship matrices, and furthermore need the phenotypic data file to estimate the polygenic component ratios and genome scanning for main and epistatic genetic effects.
All of the function modules are developed in C++ and have been successfully compiled and tested in our linux system. User can freely download, modify and compile the source code without restriction into their own pipeline.
Genotypic Data files for Additive Effect Z.txt , and Dominance Effect W.txt