. 2022 Mar 16;109(4):727–737. doi: 10.1016/j.ajhg.2022.02.015

Table 4.

Accuracy of supervised population structure inference with supplied allele frequencies on simulations

Dataset type	Base dataset	k	n	m	Supervised		Unsupervised
Dataset type	Base dataset	k	n	m	RMSE	JSD	RMSE	JSD
PSD	HGDP	6	10,000	10,000	2.9^∗	1.5^∗	5.6	3.6
PSD	TGP	6	10,000	10,000	2.0^∗	0.9^∗	3.2	1.9
PSD	TGP	6	10,000	1,000,000	0.2^∗	0.1^∗	0.3	0.2
PSD	TGP	6	100,000	1,000,000	0.2^∗	0.1^∗	0.4	0.2
PSD	TGP	6	1,000,000	1,000,000	0.2^∗	0.1^∗	0.5	0.2
Spatial	HGDP	6	10,000	10,000	2.4^∗	0.6^∗	6.5	2.6
Spatial	TGP	6	10,000	10,000	1.7^∗	0.3^∗	7.3	3.3
Spatial	TGP	10	10,000	100,000	0.6^∗	0.3^∗	6.7	5.6
Spatial	TGP	10	10,000	1,000,000	0.3^∗	0.1^∗	8.2	7.2

True allele frequencies were supplied to SCOPE to use in supervised population structure inference. Root-mean-square error (RMSE) and Jensen-Shannon divergence (JSD) were computed against the true admixture proportions. Estimated proportions of 0 were set to $1 \times 10^{- 9}$ for JSD calculations (see subjects and methods). Values are displayed in percentages and rounded to the first decimal place. Values with an asterisk denote the best value for each dataset.