R/logs_example.R

In neurogenomics/MungeSumstats: Standardise summary statistics from GWAS

#' Example logs file
#' 
#' Example logs file produced by \link[MungeSumstats]{format_sumstats}.
#' 
#' @param read Whether to read the logs file into memory. 
#' @source 
#' \code{
#' eduAttainOkbayPth <- system.file("extdata", "eduAttainOkbay.txt",
#'                                  package = "MungeSumstats")
#' sumstats_dt <- data.table::fread(eduAttainOkbayPth)
#' #### Introduce values that need to be fixed ####
#' sumstats_dt$Pval[10:15] <- 5
#' sumstats_dt$Pval[20:22] <- -5
#' sumstats_dt$Pval[23:25] <- "5e-324"
#' ss_path <- tempfile()
#' data.table::fwrite(sumstats_dt, ss_path)
#' log_folder <- tempdir()
#' reformatted <- MungeSumstats::format_sumstats(
#'     path = ss_path,
#'     ref_genome = "GRCh37",
#'     log_folder = log_folder,
#'     log_mungesumstats_msgs = TRUE,
#'     log_folder_ind = TRUE,
#' )
#' file.copy(reformatted$log_files$MungeSumstats_log_msg,
#'           "inst/extdata",overwrite = TRUE)
#' }
#' @returns Path to logs file.
#' @keywords internal
logs_example <- function(read = FALSE){ 
    logs_path <- system.file("extdata/MungeSumstats_log_msg.txt",
                             package = "MungeSumstats")
    if(read){
        l <- readLines(logs_path)
        return(l)
    } else {
        return(logs_path)
    } 
}