R/do_analysis.R

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

#' Perform analysis for the KOMODO2 workflow
#'
#' This script implements the third step of the LCFD workflow of KOMODO2.
#' It is responsible for performing the actual analysis and generating
#' all the processed data and tables.
#'
#' The script expects enriched `KOMODO2`-type lists generated after running
#' [load_data()] -> [clean_data()].
#'
#'
#' @param defs an enriched KOMODO2-type list object (see Details).
#'
#'
#' @export
#'


do_analysis <- function(defs){

  # ================== Sanity checks ==================
  assert_that(all(c("list", "KOMODO2") %in% class(defs)),
              "tree_type" %in% names(defs),
              "tree_path" %in% names(defs))

  if("MHT.method" %in% names(defs)){
    assertthat::assert_that(defs$MHT.method %in% stats::p.adjust.methods)
  } else {
    defs$MHT.method <- "BH"
  }

  # Perform analysis
  cat("\nMain Analysis:\n")
  defs <- switch(tolower(defs$type),
                 significance = do_analysis_significance(defs),
                 correlation  = do_analysis_correlation(defs))


}