R/MAIN_compare_summarize_inxight2biopax.R

In grishagin/RIGbiopax: Extract and Compare Genes and Pathways from BioPAX

MAIN_compare_summarize_inxight2biopax<-
  function(wkdir){
    
    #' @export
    #' @title
    #' Compare and Summarize Source BioPAX files to Inxight Pathways List
    #' @description 
    #' Compare genes/proteins extracted from BioPAX to inxight pathways list, and then 
    #' prepare a comprehensive summary such comparison.
    #' @param wkdir Work directory.
    
    #' @author 
    #' Ivan Grishagin
    
    ########### packages
    require(readxl)
    
    ########### workspace with biopax
    biopax_ws<-
      system.file("extdata"
                  ,"biopax_objects_current_version.RData"
                  ,package="RIGbiopax")
    load(biopax_ws
         ,envir = environment())
    
    ########### output dir
    output_dir<-
      file.path(wkdir
                ,paste0(Sys.Date()
                        ,"_RESULTS_inxight-list_VS_biopax_comparison"))
    
    ########### biopax objects
    biopax_source_names<-
      c("BioCarta"
        ,"KEGG"
        ,"NCI-Nature"
        ,"NetPath"
        ,"Wiki Pathways"
        ,"Science Signaling"
        ,"Reactome"
        ,"RMC"
      )
    biopax_obj<-
      list(biocarta_biopax
           ,kegg_biopax
           ,nci_biopax
           ,netpath_biopax
           ,wiki_biopax
           ,scisig_biopax
           ,reactome_biopax
           ,rmc_biopax
      )
    
    
    for (ondex in 1:length(biopax_obj)){
      MAIN_compare_toxdb_biopax(work_dir=wkdir
                                ,source_owl_dir=NULL
                                ,output_dir=NULL
                                ,pw_matchup_file="default"
                                ,toxdb_genes_file="default"
                                ,source_name=biopax_source_names[ondex]
                                ,owl_biopax=biopax_obj[[ondex]]
                                ,verbose=FALSE)
    }
    
    genes_df<-
      merge_gene_comparison_results(dir = output_dir
                                    ,pattern = "genes"
                                    ,filename = NULL)
    pathways_df<-
      merge_gene_comparison_results(dir = output_dir
                                    ,pattern = "pathways"
                                    ,filename = NULL)
    
    #conduct comparisons
    MAIN_biopax_toxdb_comparison_summary(output_dir=
                                           file.path(wkdir
                                                     ,"summary")
                                         ,pw_matchup_file="default"
                                         ,pw_src_file="default"
                                         ,genes_df=genes_df
    )
  }