Analysis over multiple generations

What happens if a mutation stops being selected for? 20 generations of individuals are simulated. The selection stops after 10 generations. The simulation is run 100 times.

Load packages

require(TwoSampleMR)

## Loading required package: TwoSampleMR

## TwoSampleMR version 0.5.6 
## [>] New: Option to use non-European LD reference panels for clumping etc
## [>] Some studies temporarily quarantined to verify effect allele
## [>] See news(package='TwoSampleMR') and https://gwas.mrcieu.ac.uk for further details

require(jsonlite)

## Loading required package: jsonlite

Get file path

config <- read_json("~/config.json")
mr_sel_path <- config$mr_sel_path

Use the Wald ratio to get the Biv estimate and standard error for each scenario and each generation

b_mat<-matrix(NA,100,20)
se_mat<-matrix(NA,100,20)
for (s in 1:100){
  setwd(paste0(mr_sel_path,"/Simulations/children/multigen/selStop_sim_",s))
  for (g in 0:19){
    dat<-read.table(paste0("dat_",g,".txt"),header = TRUE)
    mod1<-summary(lm(dat$pheno~dat$geno))
    bgx<-mod1$coefficients[2,1]
    segx<-mod1$coefficients[2,2]
    mod2<-summary(glm(dat$children~dat$geno,family=poisson("log")))
    bgy<-mod2$coefficients[2,1]
    segy<-mod2$coefficients[2,2]
    mrw<-mr_wald_ratio(bgx,bgy,segx,segy)
    b_mat[s,g+1]<-mrw$b
    se_mat[s,g+1]<-mrw$se
  }
}

Compare selection coefficients the generation before selection ended and the generation after selection ended

boxplot(b_mat,xlab="Generations",ylab="Estimated selection strength")
abline(h=0.05,lty=2,col="red")
abline(h=0,lty=2,col="blue")