How can I combine a kinship matrix with subset individuals when using rvtests?
Adam Locke (a collaborator of this project) suggests that removing covariate information for the unselected individuals (i.e. setting it to NA) works around this problem:


  I believe the problem is that he is using a pre-computed kinship matrix including both males and females, and when using the “—peopleIncludeFile” it can’t properly select the right people from the kinship matrix. I don’t know that others have tried to do analysis this way. An alternative, that I think has worked for others, is to generate phenotype variables that have values only for males or females (so, e.g., BMI, BMI_females, BMI_males). For whatever reason, this appears to correctly only use the and select the samples desired without the kinship matrix.


Presumably a kinship matrix that is generated for just the subset individuals will work as well, although I don't like the idea that rvtests isn't able to do a label lookup on the kinship matrix to find the correct individuals.