Changes

  % 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].

 

=== Incorporating Covariates ===

=== Incorporating Covariates ===

If one wants to adjust for covariates simultanenously, add -c [cov_file] options to the above run, with the covariate file similar to the phenotype files, but allowing multiple columns ( > 3 ). Note that the intercept has to be included, meaning that the third column is recommended to be 1 always, and the covariates needs to be included from the fourth column. The order of the individual IDs should conform to the .tfam files, similar to the phenotype files.

If one wants to adjust for covariates simultanenously, add -c [cov_file] options to the above run, with the covariate file similar to the phenotype files, but allowing multiple columns ( > 3 ). Note that the intercept has to be included, meaning that the third column is recommended to be 1 always, and the covariates needs to be included from the fourth column. The order of the individual IDs should conform to the .tfam files, similar to the phenotype files.