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Run EMMAX with the phenotype, tped/tfam files, and the kinship files as follows.
Run EMMAX with the phenotype, tped/tfam files, and the kinship files as follows.
% emmax -v -d 10 -t [tped_prefix] -p [pheno_file] -k [kin_file] -o [out_prefix]
% emmax -v -d 10 -t [tped_prefix] -p [pheno_file] -k [kin_file] -o [out_prefix]
This will generate the following files:
* [out_prefix].reml : REML output with 6 lines, where each line represents (1) Log-likelihood with variance component (2) Log-likelihood without variance component, (3) \delta = \sigma_e^2 / \sigma_g^2 (Ratio between variance parameters) (4) \sigma_g^2 (genetic variance parameter), and (5) \sigma_e^2 (residual variance parameter), and (6) The pseudo-heritability estimates
* [out_prefix].ps : Each line consist of [SNP ID], [beta], [SE-beta], [p-value].
This will generate the following files:
* [out_prefix].reml : REML output with 6 lines, where each line represents (1) Log-likelihood with variance component (2) Log-likelihood without variance component, (3) \delta = \sigma_e^2 / \sigma_g^2 (Ratio between variance parameters) (4) \sigma_g^2 (genetic variance parameter), and (5) \sigma_e^2 (residual variance parameter), and (6) The pseudo-heritability estimates
* [out_prefix].ps : Each line consist of [SNP ID], [beta], [SE-beta], [p-value].
