R/postprocess_data.R

In RajLabMSSM/echolocatoR: Automated genomic fine-mapping

postprocess_data <- function(FINEMAP_DAT,
                             loci,
                             credset_thresh,
                             consensus_thresh,
                             return_all,
                             verbose){
  if(return_all){
    messager("Returning results as nested list.",v=verbose)
    names(FINEMAP_DAT) <- loci
    FINEMAP_DAT[["merged_dat"]] <- data.table::rbindlist(
      lapply(FINEMAP_DAT, function(x){x$finemap_dat}),
      fill = TRUE,
      use.names = TRUE,
      idcol = "Locus"
    )
  } else {
    messager("Returning results as a merged data.table only.",v=verbose)
    FINEMAP_DAT <- data.table::rbindlist(FINEMAP_DAT, fill = TRUE)
    FINEMAP_DAT <- echodata::find_consensus_snps(
      dat = FINEMAP_DAT,
      credset_thresh = credset_thresh,
      consensus_thresh = consensus_thresh,
      verbose = verbose)
  }
  return(FINEMAP_DAT)
}