R/PAINTOR_merge_datasets.R

In RajLabMSSM/echofinemap: echoverse module: Fine-mapping functions

PAINTOR_merge_datasets <- function(dat_ls, 
                                   # suffixes=paste0(".",names(dat_ls)),
                                   suffixes=paste0(".",seq_len(length(dat_ls))),
                                   verbose=TRUE){ 
    
    req_cols <- c("CHR","POS","SNP","ZSCORE")
    messager("Merging list of primary datasets.",v=verbose)
    dat_merged <- lapply(names(dat_ls), 
                         function(nm){
        d <- dat_ls[[nm]]
        missing_cols <- req_cols[!req_cols %in% names(d)]
        if(length(missing_cols)>0){
            stp <- paste("Dataset",paste0("'",nm,"'"),
                         "is missing the following required column(s):",
                         paste0("\n - ",missing_cols,collapse = ""))
            stop(stp)
        }
        return(d)
        # d[,c("CHR","POS","SNP","ZSCORE")]
    }) |> Reduce(f = function(...){
        merge(..., 
              by=c("CHR","POS","SNP"),
              suffixes=suffixes)
        })
    return(dat_merged)
}