Using polygenic model and kinship matrix

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Joined: Tue May 06, 2014 4:55 am

Using polygenic model and kinship matrix

Postby zoey » Tue May 06, 2014 5:17 am

Dear GenABEL users,

We sampled 3-5 replicates for each of 27 plant genotypes, and have the trait data for all samples. We also have field conditions and sequencing runs as the covariates.

In addition, we have a kinship matrix for all the samples showing the genetic relationship of the samples, which is constructed from the SNP data of the plant genotypes.

We are not really plant breeding people, but are just looking for the plant genotype effect in the traits. GenABEL looks perfect for this aim.

To make sure we are fitting the correct model, here are a few questions that we hope you could help us with:

1) Field conditions and sequencing runs are fixed effects. What about plant genotypes? If we fit plant genotypes as a fixed effect, is it correct to include the kinship matrix as a correlated random effect for the 'kin' argument, especially when the kinship matrix is constructed based on the plant genotypes?

2) The model$esth2 gives the heritability estimation, so is it for all the fixed effects? Is it possible to parse it and obtain a heritability value for each of the fixed effect, as in our case the heritability value for the plant genotypes?

3) If the kinship matrix is constructed using identity by state SNP data, does it need to be transformed in some way to be used in the model? For example, the 'hglm' package does a Cholesky factorization on the kinship and transpose it.

Thank you very much for any comment from all of you!


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