PLOS_Genetics_EDGE_Paper

Scripts and results for simulated data

Simulation Scripts

• casecon-noise.pl for Case/Control simulation
• quant-noise.pl for Quantitative outcome simulation
• sim_updated.R - R script for simulation, used for the results found here.

PBS Scripts

These are batch file scripts used to run on the compute cluster.

runSimAll.pbs

Simulate case-control data using sim_updated.R data and run it in PLATO (using each of the 5 different encodings) on the fly, resulting in data-all-1000.

The nested structure of this folder is:

• MAF of 0.05, 0.1, 0.3, and 0.5
• Case-control ratio of 1, 2, and 3 combined with sample size of 2k, 10k, and 50k to get Case:Control simulations of:
  • 500:1500
  • 1000:1000
  • 1500:500
  • 2500:7500
  • 5000:5000
  • 5000:15000
  • 7500:2500
  • 10000:10000
  • 15000:5000
• PENDIFF values of 0.25, 0.33, and 0.45
• 57 Simulation Models
  • 6 main-effect models 6 encodings (REC, SUB, ADD, SUP, DOM, HET)
  • 21 interaction-only models based on all combinations of those 6 models (named, for example like ADD_x_DOM)
  • 21 main effects models based on all combinations of those 6 models (named, for example, like ADD_+_DOM)
  • 8 models specified by penetrance tables (HR-HR, HR-HET, HR-HA, HET-HET, HET-HA, XOR, Hyp, RHyp)
  • 1 NULL model
• PLATO results using 5 different encodings (add, dom, rec, codom, and weight (aka EDGE))
  • Each result compressed in its own folder
  • A text file reporting average pvalues across all simulations for each encoding

RunSimSNR.pbs

Simulate case-control data using sim_updated.R and run it in PLATO (using each of 5 different encodings) on the fly, resulting in data-SNR-1000 Results in data-SNR-1k-noMAF are similar, but only at a MAF of 0.05.

The nested structure of this folder is:

• 5 different SNR values (0.01, 0.025, 0.05, 0.075, 0.10)
• 4 different MAF values(0.05, 0.10, 0.30, 0.50)
• 52 Simulation Models
  • Same as above, except 18 main effects models and 19 interaction models, skipping:
    • ADD_+_HET
    • ADD_+_SUB
    • DOM_+_DOM
    • SUB_x_SUB
    • SUP_x_HET
• PLATO results using 5 different encodings

RunSim.pbs

Similar to RunSimAll.pbs, but using a single SNR of 0.05