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xihaoli / STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary
GNU General Public License v3.0
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kinship matrix #64

Closed eliu98 closed 6 days ago

eliu98 commented 6 days ago

Hi,

I am wondering if I could account for the relatedness by providing a kinship matrix in the null model? If so, how does it work? Do I still need the GRM?

Thank you! Elaine

xihaoli commented 6 days ago

Hi @eliu98,

Yes, you could account for the relatedness by providing a kinship matrix in the null model. Specifically, if pedigree information is available, then Φ is a pedigree-based kinship matrix. However, in practice, pedigree information is often unavailable or incomplete. In this case, Φ can be estimated by a (sparse) genetic relatedness matrix, for example, using FastSparseGRM.

Best, Xihao

eliu98 commented 6 days ago

Thank you!