R/meta.R

In zhangh12/ARTP3: Pathway and Gene-Level Association Test

meta <- function(summary.files, lambda = NULL, sel.snps = NULL, only.meta=TRUE, ambig.by.AF=FALSE){
  
  options <- list(ambig.by.AF=ambig.by.AF, print=TRUE)

  validate.summary.files(summary.files)
  
  lambda <- validate.lambda.summaryData(summary.files, lambda)
  
  sf <- load.summary.files(summary.files, lambda, sel.snps, options)
  if (ambig.by.AF) sf$stat <- align.ambig.meta(sf$stat)

  pos.info <- extract.position.information(sf$stat)
  
  ref.allele <- extract.reference.allele(sf$stat)
  
  conf.snps <- extract.conflictive.snps(sf$stat, ref.allele)
  
  rcs <- remove.conflictive.snps(sf$stat, ref.allele, conf.snps)
  
  merge.stat(rcs$stat, rcs$ref.allele, conf.snps, pos.info, sf$lambda, only.meta)
  
}