Covariate p values

p-values of association with each covariate are output between the standard error (se) and comments columns. The order is:

1. Columns of the --struct matrix, in order. Check the number by running h5ls on the structure matrix.
2. Covariates supplied by --covar_file and --covar_list, in the same order as columns in the file. Categorical covariates will be dummy coded, so there will be (number of categories - 1) columns for each such covariate supplied.

So if --struct was supplied with three columns (--pc from kmds), and --covar_list with 2q,3 (where column three has three possible values) the columns would be:

1. covar1_p: struct 1
2. covar2_p: struct 2
3. covar3_p: struct 3
4. covar4_p: covariate column 2
5. covar5_p: covariate column 3, category 2
6. covar6_p: covariate column 3, category 3