use grammar-gamma or grammar-gc

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Joined: Fri Sep 30, 2016 6:29 am

use grammar-gamma or grammar-gc

Postby biancaneve » Fri Feb 10, 2017 10:21 am

I wonder whether to use grammar “gamma” or grammar “gc”.
I still do not understand the difference between them.
As suggested by the Package ‘GenABEL’ (February 19, 2015) , I read the papers by Amin N, van Duijn CM, Aulchenko YS. PLoS ONE (for GRAMMAR-GC) and Svischeva G, Axenovich TI, Belonogova NM, van Duijn CM, Aulchenko YS. Nature Genetics. (for GRAMMAR-GAMMA).
However the difference when to use either method was not explained.
I tried both methods on my population,by increasing the values of h2 at each run (starting from h2 = 0.13).
These are my conclusions.
1. The three most significant markers at h2=.13 stay in the list of the top 10 for Pc1df till h2=.9999.
2. The value of Pc1df of each marker is the same using –gamma or –gc, at either h2.
3. In grammar-gc P1df is always less significant than Pc1df (WHY?)
4. In grammar-gamma P1df is always more significant than Pc1df (WHY?)
5. The effect of the minor allele (B effect) is lower in grammar-gc than in grammar-gamma.
6. The effect of the minor allele (B effect) in grammar-gc decreases as far as the value of h2 increases (WHY?)
7. The effect of the minor allele (B effect) in grammar-gamma increases as far as the value of h2 increases (WHY?)
Could anybody tell me if such results should regularly be expected or if I did anything wrong?

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