R/remove_deadend_refs.R

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

remove_deadend_refs<-
  function(biopax){
    #' @export
    #' @title 
    #' Remove Dead-End References from BioPAX
    #' @description 
    #' Takes in a BioPAX file, and removes those instances that refer 
    #' to instances that do not exist.
    #' @param biopax A BioPAX object.
    #' @author 
    #' Ivan Grishagin
    
    
    #remove hashes from property_attr_value column -- else it'll fail miserably
    biopax$dt$property_attr_value<-
      biopax$dt$property_attr_value %>% 
      striphash
    
    #candidate rows for removal
    to_remove_logi<-
      biopax$dt[,.(to_remove=
                     property_attr=="rdf:resource" & 
                     !property_attr_value %in% id)]$to_remove
    
    if(sum(to_remove_logi)>0){
      #if some rows need to be removed
      #remove them
      biopax$dt<-
        biopax$dt[!to_remove_logi]
      #and repeat to avoid situation where 
      #removal of dead references creates new ones
      biopax<-
        biopax %>% 
        remove_deadend_refs
    }
    
    return(biopax)
    
  }