R/QTL_pval_mix_GE.R

In vincentgarin/mppGxE: MPP GxE QTL analysis

###################
# QTL_pval_mix_GE #
###################

# Function to collect the p-values from MPP GxE analyses

QTL_pval_mix_GE <- function(mppData, model, nEnv, Q.eff, x, QTL.el, ref.name, par.names,
                            fct, mod) {

  if(mod == 'M3'){

    if(fct == "SIM"){
      start.ind <- 2; end.ind <- 1
    } else if(fct == "CIM") {
      start.ind <- 3; end.ind <- 2}

  } else if (mod == 'M4'){

    if(fct == "SIM"){
      start.ind <- 3; end.ind <- 2
    } else if(fct == "CIM") {
      start.ind <- 4; end.ind <- 3}

  }



  sign <- sign(rev(model$coefficients$fixed[1:QTL.el]))
  pval <- asreml::wald(model)[start.ind:(QTL.el + end.ind), 4]
  pval <- pval * sign
  pval[pval == 0] <- 1
  names(pval) <- ref.name

  if(Q.eff == "par"){

    Env_name <- rep(paste0("_E", 1:nEnv), each = length(par.names))
    par.name <- paste0(rep(par.names, nEnv), Env_name)

    pval <- pval[par.name]

  } else if (Q.eff == "anc") {

    # project into parents

    ref.all <- paste0("A.allele", mppData$par.clu[x, ])
    Env_name <- rep(paste0("_E", 1:nEnv), each = length(par.names))
    ref.all <- paste0(ref.all, Env_name)

    pval <- pval[ref.all]


  }

  return(pval)

}