R/load_data_significance.R

In fcampelo/KOMODO2-CRAN: Kegg Orthology EnrichMent Online DetectiOn

# Specific function to load data if type == "significance" in the KOMODO2
# definition list. (Not exported to to the namespace)

load_data_significance <- function(defs){

  # ================== Sanity checks ==================
  defs <- check_inputs_significance(defs)


  # ================== Process test.path  ==================

  # If path points to a file containing the paths to the genome files
  if (utils::file_test("-f", defs$test.path)) {
    defs$test.name <- utils::read.table(file         = defs$test.path,
                                        sep          = "\t",
                                        strip.white  = TRUE,
                                        comment.char = "",
                                        check.names  = FALSE,
                                        header       = FALSE,
                                        stringsAsFactors = FALSE)

    # May have the total number of elements in that genome in the second
    # column, in case the files themselves have missing elements
    if (ncol(defs$test.name) == 2) {
      defs$testElementCount <- defs$test.name[, 2]
    }
    defs$test.name <- defs$test.name[, 1]


    # If path points to a folder containing the genome files themselves
  } else if (utils::file_test("-d", defs$test.path)){
    defs$test.name <- list.files(path       = defs$test.path,
                                 all.files  = FALSE,
                                 full.names = TRUE,
                                 recursive  = FALSE)

  } else stop("test.path is neither a valid file nor a valid folder")

  # ================== Process back.path  ==================

  # If path points to a file containing the paths to the genome files
  if (utils::file_test("-f", defs$back.path)) {
    defs$back.name <- utils::read.table(file         = defs$back.path,
                                        sep          = "\t",
                                        strip.white  = TRUE,
                                        comment.char = "",
                                        check.names  = FALSE,
                                        header       = FALSE,
                                        stringsAsFactors = FALSE)

    # May have the total number of elements in that genome in the second
    # column, in case the files themselves have missing elements
    if (ncol(defs$back.name) == 2) {
      defs$backElementCount <- defs$back.name[, 2]
    }
    defs$back.name <- defs$back.name[, 1]


    # If path points to a folder containing the genome files themselves
  } else if (utils::file_test("-d", defs$back.path)) {
    defs$back.name <- list.files(path       = defs$back.path,
                                 all.files  = FALSE,
                                 full.names = TRUE,
                                 recursive  = FALSE)

  } else stop("back.path is neither a valid file nor a valid folder")


  # Read genome files
  cat("\nLoading data:\n")
  defs$test <- pbmcapply::pbmclapply(X              = defs$test.name,
                                     FUN            = utils::read.table,
                                     sep            = "\t",
                                     header         = TRUE,
                                     colClasses     = "character",
                                     strip.white    = TRUE,
                                     comment.char   = "",
                                     row.names      = 1,
                                     check.names    = FALSE,
                                     mc.preschedule = FALSE,
                                     mc.cores       = defs$cores)

  defs$back <- pbmcapply::pbmclapply(X              = defs$back.name,
                                     FUN            = utils::read.table,
                                     sep            = "\t",
                                     header         = TRUE,
                                     colClasses     = "character",
                                     strip.white    = TRUE,
                                     comment.char   = "",
                                     row.names      = 1,
                                     check.names    = FALSE,
                                     mc.preschedule = FALSE,
                                     mc.cores       = defs$cores)

  return(defs)
}