R/bp2.normalize.complexes.R

In microbiome/biopax2: BioPAX level 2 S4 object model

## Copyright (c) 2010 Ossi Koivistoinen

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bp2.normalize.complexes <- function(complexes, mapping=NULL)
{
  sub.complexes <- vector("list",length=length(complexes))
  sub.proteins <- vector("list",length=length(complexes))
  names(sub.complexes) <- names(sub.proteins) <- names(complexes)
  
  for(i in 1:length(complexes))
    {
      if (i %% 100 == 0) { cat("Complex", i, "/", length(complexes),"\n") }
      physical.entity.participants <- bp2.flatten(bp2.find.followers(complexes[[i]], include.slots="components"))
      if (length(physical.entity.participants) > 0)
        {
          sub.phys.ents <- bp2.flatten(bp2.find.followers(physical.entity.participants,include.slots=c("physicalEntity")))
          sub.complexes[[i]] <- bp2.get.instances.of(sub.phys.ents, "bp2.complex")
          sub.proteins[[i]] <- bp2.get.instances.of(sub.phys.ents, "bp2.protein")
        }
      else
        {
          cat("No physical entity participants\n")
        }
    }
  
  sub.proteins <- bp2.find.proteins(sub.proteins)
  if(!is.null(mapping))
    {
      genes <- bp2.uniprot.to.entrez(sub.proteins, mapping)
      genes <- bp2.filter.NAs.from.list.of.lists(genes)
    }
  else
    {
      genes <- NULL
    }
  
  list(names=names(complexes),
       id=sapply(complexes, function(x) {slot(x, "rdf.id")}),
       sub.complexes=sub.complexes,
       proteins=sub.proteins,
       genes=genes)
}