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Ancestry-informative transcripts were identified using a rank-score-based multivariate association test, and ancestry-informative eQTL were identified using Fisher's exact test.
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While FBAT can perform univariate or multivariate association tests, EIGENSTRAT can only perform univariate tests.
Another feature of the proposed method that can improve statistical power is the ability to perform multivariate association tests.
For genetic association studies, methods have also been proposed for performing multivariate association tests on unrelated samples [43] and on families [44], separately.
In this study, we propose a simple approach to perform univariate or multivariate association tests when correcting for population stratification with data generated by combining unrelated samples and nuclear families.
In this study, by extending generalized estimating equations (GEEs), we propose a simple approach for performing univariate or multivariate association tests for the combined data of unrelated subjects and nuclear families.
Results: Here we present a new method, multivariate gene-based association test by extended Simes procedure (MGAS), that allows gene-based testing of multivariate phenotypes in unrelated individuals.
From a list of results of the association test for a multivariate phenotype, false positives of SNPs are pruned by the following conditions and significant ones remain: (1) P-values for an association test of multivariate phenotype ≤ 5×10-4 5×10-4RPyi ≥ 1 and mORpyj ≥ 1 (3) P-value of an indexed SNP ≤ 10-5 and p-values of clumped SNPs ≤ 10-4 in order to evaluate formation of LD.
We develop family-based functional principal-component analysis (FPCA) with or without smoothing, a generalized T2, combined multivariate and collapsing (CMC) method, and single-marker association test statistics.
Methods based on genotype similarity include the following: sequence kernel association test (SKAT) [ 11]; kernel-based association test (KBAT) [ 18], multivariate distance matrix regression test (MDMR) [ 19]; and aggregate U-test [ 20].
Multivariate association analysis.
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