Question about null model

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aldi

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May 12, 2022, 3:34:41 PM5/12/22
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Hi Chris and other colleagues.
I am working on a model which we call it null model.
This means, I have a quantitative trait as a response variable. I have also sex, age, age2 and GRM (genetic relationship matrix, produced via plink2, via option --make-rel square --out a_grm). The output of GRM matrix is tab-delimited with no column-names or row-names, but it has another file with header #iid, which has all IDs of individuals included in the GRM matrix, with more than 3,000 subjects. The response length with more than 2,000 subjects.

So, my questions are
1. Can I use PLINK2 to produce the residuals from the following model:
response ~ age + age2+ PC1+...+ PC10 + GRM ?  If yes how to implement it in PLINK2?

2. Can I estimate the trait (response, quantitative) heritability by using the estimated GRM matrix? The design of individuals is in families, and I have checked the results of GRM match for example, coefficients of relationship of parents offspring are about 0.5, while of two parents are about 0. The data are sequence data, and for GRM I have used about 120,000 best variants of autosome with MAF >= 0.45.
Thank you in advance for any response.

Aldi

Christopher Chang

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May 14, 2022, 3:21:11 PM5/14/22
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No, PLINK2 does not support linear mixed model analysis; you should another software package for this.
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