search

syntheke / bayesR

Bayesian hierarchical model for complex trait analysis
45 stars 26 forks source link

How to adjust the proportion of SNPs with no additive effect ? #5

Closed Feng-Zhang closed 6 years ago

Feng-Zhang commented 7 years ago
  1. After running BayesR with default parameters, the proportion of SNPs from 4 distribution (variance equals 0,0.0001,0.001,0.01) approximately are 0.84, 0.15, 0.005, 0.0006, respectively. But I want to compare the difference of prediction using BayesR and BayesB, so when running BayesR, the proportion of SNPs with 0 varience should be set as 0.95, as same as π using BayesB.
  2. “-delta 2” sets the prior to 2 for all mixture components. But what exactly is the parameter meaning? If the number is larger, how does it affect the result of genomic prodiction?

Could you please tell me how to set the proportion? Any suggestions or tips would be greatly appreciated.

syntheke commented 7 years ago

In BayesB each SNP has its own variance and such models are not implemented in BayesR. Check out the chapter by Fernando and Garrick in "Genome-Wide Association Studies and Genomic Prediction" for R code of BayesB.

Feng-Zhang commented 7 years ago

In BayesR 84% of SNPs has variance 0 from the result I ran and 95% of SNPs has no effect in BayesB. What is the difference I did not notice?
I just want to adjust the proportion of SNPs with no effect, so that the two model are comparable. In other word, if possible to adjust some paremeter in BayesR, giving more wegith for first distribution as prior information, so that the proportation of SNPs with variance 0 reach 95% ?

The parameter "delta", prior for Dirichlet , affect the proportion of SNPs effect. But I am not sure the prior inforatmtin can affect the final result ? Or do not affect the reuslt but only the convergence speed?

GabrieleNocchi commented 5 years ago

This was a good question: The parameter "delta", prior for Dirichlet , affect the proportion of SNPs effect. But I am not sure the prior inforatmtin can affect the final result ? Or do not affect the reuslt but only the convergence speed?

It would be nice to know more.