R/clean_data_significance.R

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

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

clean_data_significance <- function(defs){

  # Set the names of defs$test and defs$back
  defs$test.name   <- basename(defs$test.name)
  defs$back.name   <- basename(defs$back.name)
  names(defs$test) <- defs$test.name
  names(defs$back) <- defs$back.name

  # Safety check, removes the counts if any value is missing
  if (!is.null(defs$testElementCount)) {
    names(defs$testElementCount) <- defs$test.name
    if (any(is.na(defs$testElementCount))) {
      defs$testElementCount <- NULL
    }
  }
  if (!is.null(defs$backElementCount)) {
    names(defs$backElementCount) <- defs$back.name
    if (any(is.na(defs$backElementCount))) {
      defs$backElementCount <- NULL
    }
  }

  # Parse Genome Maps
  defs$test.anno <- pbmcapply::pbmclapply(X              = defs$test,
                                          FUN            = parse_GenomeMap,
                                          column         = defs$column,
                                          mc.preschedule = FALSE,
                                          mc.cores       = defs$cores)

  defs$back.anno <- pbmcapply::pbmclapply(X              = defs$back,
                                          FUN            = parse_GenomeMap,
                                          column         = defs$column,
                                          mc.preschedule = FALSE,
                                          mc.cores       = defs$cores)

  # Remove test and back fields from defs
  defs$test <- NULL
  defs$back <- NULL

  return(defs)
}