Fernandes, Samuel B.; Zhang, Kevin, S.; Jamann, Tiffany M.; Lipka, Alexander E. Frontiers in Genetics (2021). https://www.frontiersin.org/article/10.3389/fgene.2020.602526
The following files contain:
pipeline_ST.R: Pipeline to simulate and analyze ST scenarios
pipeline_LD.R: Pipeline to simulate and analyze LD (Spurious Pleiotropy) scenarios
pipeline_P.R: Pipeline to simulate and analyze P scenarios
run_simulation_ST.R, run_simulation_LD.R, run_simulation_P.R: Functions to call simplePHENOTYPES in each genetic architecture
gemma.R: a wrapper to run the software GEMMA from R.
run_gemma_ST, run_gemma_LD, run_gemma_P: Function to call gemma.R in each genetic architecture
graphs_combined.R: scripts used to generate all figures. Figures for different distances or FDR were generated with the same script by changing the file with the dataset.
data: Marker data and kinship information for each dataset used in the simulation
It is necessary to create a folder named 'simulation' containing subfolders named 'ST', 'LD', and 'P' to run the pipeline script.
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