R/internal_add_biopax_ids.R

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

internal_add_biopax_ids<-
  function(all_pathways
           ,pw_biopax){
    
    #' @keywords internal
    
    #add biopax pathway ids
    all_pathways_pwid<-
      adply(.data = as.data.frame(all_pathways)
            ,.margins = 1
            ,.fun = function(dfrow){
              biopaxID<-
                pw_biopax$biopax.Pathway.ID[pw_biopax$biopax.Pathway.Name %chin% 
                                              dfrow$biopax.Pathway.Name]
              dfrow<-
                dfrow %>%
                .[rep(1,length(biopaxID)),] %>%
                mutate(biopax.Pathway.ID=biopaxID)
              
              if(length(biopaxID)>1) {
                message("add_biopax_ids: Found "
                        ,length(biopaxID)
                        ," IDs for "
                        ,unique(dfrow$biopax.Pathway.Name))
              }
              return(dfrow)
              
            })
    return(all_pathways_pwid)
  }