Table 5 Comparison of probabilities that causal variants (cvs) have rank 10 or less, from flashfm and fastPAINTOR, varying sample size.

From: The flashfm approach for fine-mapping multiple quantitative traits

 

Trait 1 (E+G)

 

Pr(1 or more cvs rank <= 10)

Pr(Both cvs rank <= 10)

N

flashfm

fastPAINTOR

flashfm

fastPAINTOR

1000

0.797

0.493

0.243

0.083

2000

0.937

0.757

0.530

0.187

3000

0.987

0.823

0.677

0.303

4000

1.000

0.870

0.847

0.403

5000

0.997

0.887

0.867

0.457

 

Trait 2 (E+H)

 

Pr(1 or more cvs rank <= 10)

Pr(Both cvs rank <= 10)

N

flashfm

fastPAINTOR

flashfm

fastPAINTOR

1000

0.747

0.463

0.133

0.057

2000

0.917

0.617

0.370

0.130

3000

0.960

0.737

0.600

0.237

4000

0.987

0.783

0.717

0.297

5000

0.997

0.857

0.783

0.353

  1. For all sample sizes, flashfm consistently has larger probabilities than those from fastPAINTOR. Flashfm has twice the probability of fastPAINTOR for both causal variants to have rank 10 or lower. Two traits were simulated to have causal variants E+G and E+H and trait correlation is 0.4. Sample size ranges from N = 1000 to 5000. The region has 1231 SNPS and was simulated to mimic the LD structure of the CTLA4 region, 2q-204446258-204816382 (GRCh37/hg19). Results are based on 300 replications.
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