R/get_magma_paths.r

In NathanSkene/MAGMA_Celltyping: Find Causal Cell-Types Underlying Complex Trait Genetics

#' Get MAGMA Paths
#'
#' Gets paths to folders based on location of the GWAS summary statistics file. 
#' This avoids the GWAS sumstats folder becoming a mess.
#'
#' @param gwas_sumstats_path Path to the GWAS summary statistics file.
#' @param upstream_kb How many kb upstream of the gene 
#' should SNPs be included?
#' @param downstream_kb How many kb downstream of the gene 
#' should SNPs be included?
#' @param output_path If being called from 
#' \link[MAGMA.Celltyping]{magma_tileplot} 
#' then \code{gwas_sumstats_path} cannot be specified, 
#' so instead specificity the base folder where MAGMA_Figures exists.
#'
#' @return File path for where MAGMA files should be created
#'
#' @source 
#' \code{
#' gwas_sumstats_path <- MAGMA.Celltyping::get_example_gwas(
#'     trait = "educational_attainment")
#' magmaPaths <- MAGMA.Celltyping:::get_magma_paths(
#'     gwas_sumstats_path = gwas_sumstats_path, 
#'     upstream_kb = 35, 
#'     downstream_kb = 10)
#' }
#' @export
get_magma_paths <- function(gwas_sumstats_path = NA,
                            upstream_kb = NA,
                            downstream_kb = NA,
                            output_path = NA) {
  # devoptera::args2vars(get_magma_paths)
  
  # Error checking
  if ((is.null(gwas_sumstats_path) || is.na(gwas_sumstats_path) ) &&
      is.na(output_path)) {
      stop("Either gwas_sumstats_path or output_path must be specified")
  }
  if (!is.null(gwas_sumstats_path) &&
      !is.na(gwas_sumstats_path) &&
      (is.na(upstream_kb) |
          is.na(downstream_kb))) {
      stop(paste(
          "If gwas_sumstats_path is specified then upstream_kb",
          "and downstream_kb must also be specified"
      ))
  }
  # If output_path is not specified, 
  # then use the folder containing gwas_sumstats
  if (is.na(output_path)) {
      output_path <- dirname(gwas_sumstats_path)
  }
  output_path <- fix_path(output_path)
  dir.create(output_path, showWarnings = FALSE, recursive = TRUE) 

  if (!is.na(gwas_sumstats_path)) {
      gwas_sumstats_path <- fix_path(gwas_sumstats_path)
      gwasFileName <- basename(gwas_sumstats_path)
      # Set the paths
      pathMagmaFiles <- sprintf(
          file.path("%s","MAGMA_Files","%s.%sUP.%sDOWN"),
          output_path, gwasFileName, upstream_kb, downstream_kb
      )
      pathFigs <- sprintf(
          file.path("%s","MAGMA_Figures","%s","FIGS"),
          output_path, gwasFileName
      )
      pathTiles <- sprintf(
          file.path("%s","MAGMA_Figures","Tileplots"),
          output_path
      )
      # Normalize paths  
      pathMagmaFiles <- fix_path(pathMagmaFiles)
      pathTiles <- fix_path(pathTiles)
      pathFigs <- fix_path(pathFigs)  
      # Create the folders (in case they don't exist yet) 
      dir.create(pathMagmaFiles, showWarnings = FALSE, recursive = TRUE) 
      dir.create(pathTiles, showWarnings = FALSE, recursive = TRUE)
      dir.create(pathFigs, showWarnings = FALSE, recursive = TRUE)

      prefix <- fix_path(
          sprintf("%s.%sUP.%sDOWN",
                  gwasFileName, 
                  upstream_kb, 
                  downstream_kb)
      )
      filePathPrefix <- sprintf(file.path("%s","%s.%sUP.%sDOWN"),
                                pathMagmaFiles, gwasFileName,
                                upstream_kb, downstream_kb)
      filePathPrefix <- fix_path(filePathPrefix)
      # Return the paths
      magmaPaths <- list(tiles = pathTiles,
                         figs = pathFigs, 
                         files = pathMagmaFiles,
                         prefix = prefix, 
                         filePathPrefix = filePathPrefix, 
                         gwasFileName = gwasFileName, 
                         gwasFilePath = gwas_sumstats_path)
  } else { 
      pathTiles <- fix_path(
          sprintf(file.path("%s","MAGMA_Figures","Tileplots"), output_path)
      )
      pathFigs <- fix_path(
          sprintf(file.path("%s","MAGMA_Figures"), output_path)
      )   
      dir.create(pathTiles, showWarnings = FALSE, recursive = TRUE)
      dir.create(pathFigs, showWarnings = FALSE, recursive = TRUE)
      magmaPaths <- list(tiles = pathTiles,
                         figs = pathFigs)
  } 
  return(magmaPaths)
}

get.magma.paths <- function(...){
    .Deprecated("get_magma_paths")
    get_magma_paths(...)
}