R/report_summary.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

#' Report info on current state of the summary statistics
#'
#' Prints report.
#'
#' @return No return
#'
#' @param sumstats_dt data table obj of the summary
#'  statistics file for the GWAS.
#' @keywords internal
report_summary <- function(sumstats_dt,
                           orig_dims = NULL) {
    ### Add this to avoid confusing BiocCheck
    P <- NULL

    orig_dims_report <- if (!is.null(orig_dims)) {
        paste0(" (", round(nrow(sumstats_dt) / orig_dims[1] * 100, 1),
               "% of original ", 
               formatC(orig_dims[1], big.mark = ",", format = "fg"),
               " rows)")
    } else {
        NULL
    }

    rows_msg <- paste0("\n   - ",
                       formatC(nrow(sumstats_dt), 
                               big.mark = ",", format = "fg"),
                       " rows", orig_dims_report)
    SNP_msg <- if ("SNP" %in% colnames(sumstats_dt)) {
        paste0("\n   - ", 
               formatC(length(unique(sumstats_dt$SNP)),
                       big.mark = ",", format = "fg"),
               " unique variants")
    } else {
        NULL
    }
    P_msg <- if ("P" %in% colnames(sumstats_dt)) {
        if (!is.numeric(sumstats_dt$P)){
          sumstats_dt[,P:=as.numeric(P)]
        }
        paste0("\n   - ", 
               formatC(nrow(subset(sumstats_dt, P < 5e-8)),
                       big.mark = ",", format = "fg"),
               " genome-wide significant variants (P<5e-8)")
    } else {
        NULL
    }
    CHR_msg <- if ("CHR" %in% colnames(sumstats_dt)) {
        paste0("\n   - ", 
               formatC(length(unique(sumstats_dt$CHR)),
                       big.mark = ","), 
               " chromosomes")
    } else {
        NULL
    }

    message(
        "Summary statistics report:",
        rows_msg,
        SNP_msg,
        P_msg,
        CHR_msg
    )
}