Table 1.

Method performance summary

Method#	Method	Known variants/genes used	Function effect	Accuracy†	Precision†	Recall†	MCC†
1.1	GRS	Heit et al. (3 loci)	No	37.9%	100.0%	3.0%	0.105
1.2	GRS	Heit et al. and PROS1 variants	No	47.6%	68.8%	33.3%	0.065
1.3	GRS+warfarin dose	Heit et al. and PROS1 variants	No	50.5%	89.5%	25.8%	0.252
2	Kmodes clustering	Level 1, 2 genes	No	52.4%	62.3%	65.2%	0.052
3	Kmeans clustering	Level 1, 2, 3 genes	variant-level	62.1%	70.8%	69.7%	0.182
4	Kmeans clustering	Level 1, 2, 3 genes	protein-level	58.3%	65.8%	72.7%	0.054

^†Overall accuracy (Eqn. 3), precision and recall (Eqn. 4), and MCC (Eqn. 5). Default cutoff of 0.5 was used for calling an exome VTE or non-VTE. The best performance among four methods is indicated in bold.