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

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xiekunwhy opened this issue Jun 26, 2023 · 1 comment

xiekunwhy commented Jun 26, 2023

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 Jul 17, 2024

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)

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