R/save_tsv_files.R

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

save_tsv_files <- function(defs){

  cat("\nSaving results to files: ")
  if (!dir.exists(defs$output_dir)) dir.create(defs$output_dir,
                                               recursive = TRUE,
                                               showWarnings = FALSE)

  fieldnames <- c(paste0("correlations.",
                         c("pearson", "spearman", "kendall")),
                  paste0("results.correlations.pvalue.",
                         c("pearson", "spearman", "kendall")))

  filenames  <- paste0(defs$output_dir, "/",
                       c(paste0(c("p", "s", "k"), "_corr_results.tsv"),
                         paste0(c("p", "s", "k"), "_corr_qvalues_results.tsv")))

  for (i in seq_along(fieldnames)){
    print_c_results(correlations = defs[[fieldnames[i]]],
                    annotation   = defs$annotation.cor,
                    outputName   = filenames[[i]],
                    ontology     = defs$ontology)
  }

  print_c_results(correlations = defs$contrasts.corrected,
                  annotation   = defs$annotation.contrasts,
                  outputName   = paste0(defs$output_dir,
                                        "/contrasts_corrected.tsv"),
                  ontology     = defs$ontology)

  print_c_results(correlations = defs$contrasts,
                  annotation   = defs$annotation.contrasts,
                  outputName   = paste0(defs$output_dir,
                                        "/contrasts_raw.tsv"),
                  ontology     = defs$ontology)

  print_c_results(correlations = defs$sum,
                  annotation   = defs$annotation.sum,
                  outputName   = paste0(defs$output_dir,
                                        "/sum.tsv"),
                  ontology     = defs$ontology)

  print_c_results(correlations = defs$sd,
                  annotation   = defs$annotation.sd,
                  outputName   = paste0(defs$output_dir,
                                        "/sd.tsv"),
                  ontology     = defs$ontology)

  print_c_results(correlations = defs$cv,
                  annotation   = defs$annotation.cv,
                  outputName   = paste0(defs$output_dir,
                                        "/cv.tsv"),
                  ontology     = defs$ontology)

  cat(" done!\n")
}