#' List munged summary statistics
#'
#' Searches for and lists local GWAS summary statistics files munged by
#' \link[MungeSumstats]{format_sumstats} or
#' \link[MungeSumstats]{import_sumstats}.
#'
#' @param save_dir Top-level directory to recursively search
#' for summary statistics files within.
#' @param pattern Regex pattern to search for files with.
#' @param ids_from_file Try to extract dataset IDs from file names.
#' If \code{FALSE}, will infer IDs from the directory names instead.
#' @param verbose Print messages.
#'
#' @returns Named vector of summary stats paths.
#'
#' @examples
#' save_dir <- system.file("extdata",package = "MungeSumstats")
#' munged_files <- MungeSumstats::list_sumstats(save_dir = save_dir)
#'
#' @export
#' @importFrom stats setNames
list_sumstats <- function(save_dir = getwd(),
pattern = "*.tsv.gz$",
ids_from_file = TRUE,
verbose = TRUE){
munged_files <- list.files(path = save_dir,
pattern = pattern,
full.names = TRUE,
recursive = TRUE)
#### Exclude log files ####
munged_files <- munged_files[basename(dirname(munged_files))!="logs"]
#### infer IDs ####
if(ids_from_file){
ids <- gsub(paste(supported_suffixes(),collapse = "|"), "",
basename(munged_files))
}else {
ids <- basename(dirname(munged_files))
}
#### Report ####
messager(length(munged_files),"file(s) found.",v=verbose)
return(stats::setNames(munged_files,ids))
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.