Table 3.
Population Structure Inference Results for HapMap MXL and ASW
| R2 Values | ||||||
|---|---|---|---|---|---|---|
| Ancestry | da | PC-AiR | EIGENSOFTb | MDSc | FamPCAd | ADMIXTUREe |
| MXL Sample | ||||||
| European | 1 4 10 |
0.975 – – |
0.664 0.914 0.924 |
0.751 0.935 0.943 |
0.649 0.969 0.970 |
0.640 – – |
| Native American | 1 4 10 |
0.977 – – |
0.661 0.908 0.911 |
0.748 0.929 0.932 |
0.651 0.968 0.969 |
0.633 – – |
| MXL + ASW Sample | ||||||
| European | 2 4 10 |
0.988 – – |
0.858 0.868 0.963 |
0.892 0.899 0.970 |
0.862 0.878 0.987 |
0.615 – – |
| Native American | 2 4 10 |
0.995 – – |
0.953 0.958 0.987 |
0.962 0.967 0.989 |
0.951 0.961 0.996 |
0.866 – – |
| African | 2 4 10 |
0.999 – – |
0.996 0.996 0.999 |
0.997 0.997 0.999 |
0.997 0.997 0.999 |
0.990 – – |
Population structure inference results from each method were compared to ancestry estimates from a supervised individual ancestry analysis with ADMIXTURE including reference population panels.
a
d denotes the number of axes of variation included as predictors in the linear regression model to determine the R2 value for each of the methods.
b
PCA was performed with the EIGENSOFT software.
c
MDS was implemented in the PLINK software.
d
FamPCA is the Zhu et al. [2008] method as implemented in the KING [Manichaikul et al., 2010] software.
e
An unsupervised ADMIXTURE analysis was conducted without including reference population panels. FRAPPE results were identical to ADMIXTURE.