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Based on cross-validation, both PC-Select and FaST-LMM Select chose to use all markers.
Although PC-Select and FaST-LMM Select chose to use all SNPs and thus neither method inflated statistics, we emphasize that without a priori knowledge about the genetic architecture, PC-Select automatically tunes the number of SNPs to include in the GRM to optimize power and simultaneously protects against population stratification at no cost to power.
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