inst/examplesummaryCS.R

In GCPBayes: Bayesian Meta-Analysis of Pleiotropic Effects Using Group Structure

############################# Gene DNAJC1 ###############################################
data(DNAJC1)
Breast <- DNAJC1$Breast
Thyroid <- DNAJC1$Thyroid
genename <- "DNAJC1"
snpnames <- Breast$snp
Betah <- list(Breast$beta, Thyroid$beta)
Sigmah <- list(diag(Breast$se^2), diag(Thyroid$se^2))
K <- 2
m <- 14

pvalue <- matrix(0, K, m)
for (k in 1:K) {
  pvalue[k, ] <- 2 * pnorm(-abs(Betah[[k]] / sqrt(diag(Sigmah[[k]]))))
}

zinit <- rep(0, K)
for (j in 1:K) {
  index <- 1:m
  PVALUE <- p.adjust(pvalue[j, ])
  SIGNALS <- index[PVALUE < 0.05]
  modelf1 <- rep(0, m)
  modelf1[SIGNALS] <- 1
  if (max(modelf1) == 1) (zinit[j] <- 1)
}

set.seed(123)
RES <- CS(Betah, Sigmah,
  kappa0 = 0.5, tau20 = 1, zeta0 = zinit,
  m = m, K = K, niter = 2000, burnin = 1000, nthin = 2, nchains = 1, a1 = 0.1, a2 = 0.1,
  c1 = 0.1, c2 = 0.1, sigma2 = 10^-3, snpnames = snpnames, genename = genename
)
summaryCS(RES)