stepwiseqtl() seems to get messed up with X chr QTL if sex (or presumably cross direction) are included as covariates. I think it has to do with the treatment of the null LOD when X chr QTL are included versus not.
Solution is maybe to force inclusion of null covariates like sex and cross direction whenever the X chr is included among the chromosomes being searched.
kbroman
commented
3 years ago
stepwiseqtl()seems to get messed up with X chr QTL if sex (or presumably cross direction) are included as covariates. I think it has to do with the treatment of the null LOD when X chr QTL are included versus not.Solution is maybe to force inclusion of null covariates like sex and cross direction whenever the X chr is included among the chromosomes being searched.