. Author manuscript; available in PMC: 2015 Nov 18.

Published in final edited form as: Ann Appl Stat. 2015 Nov 2;9(3):1533–1548. doi: 10.1214/15-AOAS836

Table 2.

Validity and Efficiency of Conditional Test

Mean # Mutations Per Tumor	Clonality Signal	Mean # Matching Mutations	Frequency of p<0.05¹
Mean # Mutations Per Tumor	Clonality Signal	Mean # Matching Mutations	Unconditional Test (Calibrated)	Conditional Test	Conditional Test (Calibrated)
5	0.0	0.10	0.05	0.01	0.05
5	0.1	0.56	0.41	0.36	0.40
5	0.25	1.32	0.72	0.65	0.70
10	0.0	0.21	0.05	0.02	0.05
10	0.1	1.17	0.60	0.57	0.59
10	0.25	2.60	0.92	0.89	0.90
20	0.0	0.45	0.04	0.03	0.05
20	0.1	2.41	0.83	0.81	0.82
20	0.25	5.28	0.99	0.99	0.99

Each row of the table involved a simulation with 10,000 markers in which the reference distribution for the test involved sampling from the null distribution 5000 times, and in which the test was repeated 1000 times to estimate the size (when the clonality signal is 0) or power (when the clonality signal is >0). The marginal frequencies were constructed in the following way:- For configurations with 5 mutations per tumor 10 of the loci had a marginal probability of 0.10 and the remaining 9990 had a marginal probability of 0.0004. For configurations with 10 mutations per tumor 20 of the loci had a marginal probability of 0.10 and the remaining 9980 had a marginal probability of 0.0008. For configurations with 20 mutations per tumor 20 of the loci had a marginal probability of 0.10 and the remaining 9960 had a marginal probability of 0.00016.