I would like to include the X Chromosome in a GWAS of a continuous trait which has been measured in a dataset of related individuals (same-sex twins, ~22% males, 78% females).
I had a look at the literature, but most of the approaches presented seems to focus on case-control studies rather than on continuous traits. While some studies use PLINK, I am not sure it models X-inactivation correctly. Moreover, PLINK does not handle the presence of related individuals. Usually, we take inter-individual kinship into account by using LMMs, as implemented in GEMMA. However, I do not understand whether X-inactivation is or can be modelled in GEMMA.
Does anyone has any suggestion, or knows of any paper dealing with this?
Thank you very much in advance!