Results of association analysis by different methods based on a single simulated dataset.

<p>Association strength 0.8 and threshold for the QTN were used. (A) The correlation coefficient matrix of traits. It contains three blocks of correlated traits of sizes 3, 3, and 4, respectively. (B) The correlation coefficient matrix in (A) thresholded at . The black pixels in the lower triangular part of the matrix indicate edges included in GFlasso. (C) The true regression coefficients and sparsity pattern used in simulation. (D) , where were obtained from single-SNP permutation tests performed for each phenotype separately. (E) Black pixels indicate SNP-trait pairs with significant association at based on the results of in (D). Values of the estimated regression coefficients are shown for (F) ridge regression, (G) PCA-based regression, (H) lasso, (I) , (J) , and (K) . In Panels (C)–(K), rows correspond to SNPs, and columns to phenotypes. Columns for traits in (C)–(K) are aligned with the columns in (A) and (B).