During the import process, HPlus asks you to specify covariate information in your data file. The method for specifying covariate data is the same as for grouping data. If there are no covariates, simply leave the input boxes blank.
If you have one or more covariates and specified them at import time, they will be displayed in the bottom-right frame once the data has been imported:
Initially, you are shown a lost of the covariate names with a checkbox to the left of each name. These checkboxes allow you to select one or more of the covariates to include in the analysis:
There is also a set of checkboxes to the right of the covariate names. These check-boxes are initially disabled, but when a covariate is selected for inclusion by using its left-hand check-box then the corresponding right-hand check-box is enabled, as shown in the image above. This second column of boxes is labeled 'Include for gene-env interaction'. Choosing a covariate in this column will therefore include an analysis of gene-environment interaction for that covariate.
Note: You may wish to run your analysis without gene-environment interaction first. If you find your haplotypes have low frequencies then you may be unable to get convergence in the gene-environment interaction.
 Grouping Markers |  Saving the Results |