R/complete.sum.stat.R

In zhangh12/ARTP2: Pathway and Gene-Level Association Test

complete.sum.stat <- function(sum.stat, options){
  
  msg <- paste("Calculating P and SE if not provided:", date())
  if(options$print) message(msg)
  
  nf <- length(sum.stat$stat)
  lambda <- sum.stat$lambda
  
  deleted.snps <- NULL
  for(i in 1:nf){
    
    st <- sum.stat$stat[[i]]
    id.no.SE <- which(is.na(st$SE))
    id.no.P <- which(is.na(st$P))
    
    if(length(id.no.SE) > 0){
      z2 <- qchisq(st$P[id.no.SE], df = 1, lower.tail = FALSE)
      st$SE[id.no.SE] <- abs(st$BETA[id.no.SE]/sqrt(z2))
    }
    
    st$SE <- sqrt(lambda[i]) * st$SE
    st$P <- pchisq((st$BETA/st$SE)^2, df = 1, lower.tail = FALSE)
    
    lack.info.id <- which(apply(st[, c('BETA', 'SE', 'P')], 1, function(u){sum(is.na(u)) > 0}))
    if(length(lack.info.id) > 0){
      deleted.snps <- c(deleted.snps, st[lack.info.id, 'SNP'])
    }
    
    sum.stat$stat[[i]] <- st
    rm(st)
    gc()
  }
  
  list(sum.stat = sum.stat, deleted.snps = deleted.snps)
  
}