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Covariate p values

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John Lees edited this page Mar 16, 2016 · 1 revision

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
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