jiabowang/gbye-xinrui

Effect model of gene-environment interaction, involved in predictive analysis of GWAS and GS

GbyE

Effect model of gene-environment interaction, involved in predictive analysis of GWAS and GS

Introduction

Here is a small function package related to gbye operation, which helps to run gbye programs more conveniently
This currently includes:

GbyE.R

Gbye main package, coordinate other function packages for GWAS and GS operations, sometimes, We need to prepare documents, including

• GD (Genotype file,type [0,1,2])
• GM (SNP marker map file with SNP names, Chrosome and Position)
• Y (Phenotype file,If the model phenotype is not used and the real phenotype prediction is directly used, please enter this file)
• ha2 (Heritability of the simulate phenotype)
• cov_g (Genetic correlation of the simulate phenotyp)
• NQTN (Number of phenotype related SNPs simulated, defult=20)
• nrep (Number of iterations)
• nfold (CV Multiple cross validation)
• nIter & burnIn (set Markov chain length of the R packages "BGLR")
• gwas (defult=T, Whether to perform GWAS operation)
• gs (defult=T, Whether to perform GS operation)
• file.output (Whether the operation result file is output)
• plot (Whether curve drawing is carried out on the results can show the prediction accuracy of the results)

G&E_Simulation.R

Function package for phenotypic simulation according to genotype file

GbyE.file.Calculate.R

Gbye file is generated from the original genotype file and SNP map file to show the effect of gene environment interaction

Power.FDR.Calculate.R

Calculate the FDR and Power values of the prediction results

Comparison.GWAS.Result.PValue.R

In GWAS operation, compare the pvalue value of the same SNP and screen the most significant p value for subsequent GS prediction