how to add kinship matrix

[zhoudreames]

In the matirxEQTL tutorial, this process does not add a kinship matrix to run the eQTL analysis. However, My data is family-level, and I want to add the kinship to run the eQTL analysis, How to do it? Thanks~

[zhoudreames]

@andreyshabalin I am so sorry to disturb you, can you help me, Thanks~

[andreyshabalin]

Hi @zhoudreames,

Matrix eQTL does not fully support linear mixed models. I suggest you run it without using a kinship matrix with a liberal p-value threshold and then run linear mixed model on top gene-SNP pairs to get precise p-values.

Andrey

[zhoudreames]

Thanks~