Why the diagonal of relatedness matrix is not equal to 1 or a constant value?

genetics-statistics / GEMMA

Genome-wide Efficient Mixed Model Association

https://github.com/genetics-statistics/GEMMA

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Why the diagonal of relatedness matrix is not equal to 1 or a constant value? #277

Open xiekunwhy opened 1 year ago

xiekunwhy commented 1 year ago

Hi,

Why the diagonal of relatedness matrix generated by gemma is not equal to 1 or a constant value? Column-wise centralization results?

Best, Kun

johanzi commented 4 months ago

The centered relatedness matrix does not scale each column of the genotype matrix, so the main diagonal of the resulting relatedness matrix will not be close to 1s (usually around 0.3 depending on maf etc.). If you use the scaled relatedness matrix (.sXX), then the main diagonal should be made of values that are very close to 1s. (https://groups.google.com/g/gemma-discussion/c/34FyII8oXUM)