R/load_inxight_genes_per_source.R

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

load_inxight_genes_per_source<-
  function(source_name
           ,toxdb_genes_file=NULL
           ,all_pathways){
    
    #' @export
    #' @title
    #' Load Dataframe with Genes/Pathways
    #' @description 
    #' Load a table with all genes listed for each of the pathways.
    #' @param source_name Name of the BioPAX source.
    #' @param toxdb_genes_file File that has a table of all genes listed for all pathways. 
    #' @param all_pathways Dataframe with all desired pathways.
    
    #' @author 
    #' Ivan Grishagin
    
    #list of genes and pathways
    #and select only pertaining columns
    options(stringsAsFactors = FALSE)
    
    toxdb<-read.table(toxdb_genes_file
                      ,header = TRUE
                      ,quote=""
                      ,sep="\t") %>% 
      dplyr::select(toxdb.Pathway.ID=Pathway.ID
                    ,toxdb.Pathway.Name=Pathway.Name
                    ,toxdb.Gene.ID=Gene.ID
                    ,toxdb.Gene.Symbol=Gene.Symbol) 
    #pathway name and gene symbol identifiers -> to lower case
    toxdb$toxdb.Pathway.Name<-
      tolower(toxdb$toxdb.Pathway.Name)
    
    #get a subset of toxdb for just one source (as featured in Ruili's list of curated pathways)
    toxdb<-
      toxdb %>%
      subset(.$toxdb.Pathway.ID %in% all_pathways$toxdb.Pathway.ID) %>%
      mutate(Source=source_name)
    
    return(toxdb)
  }