R/omit.R

In sbstatgen/GKnowMTest: Genomic Knowledge-guided Multiple Testing

fn.hash<-function(tt)
{
  u1<-unique(tt)
  hash<-rank(u1)
  names(hash)<-u1
  tt2<-unname(hash[as.character(tt)])
  
  return(tt2) 
}


omit<-function(ob,val)
{
  if(is.character(val))
  {
    rn<-rownames(ob@snp.df)
    miss<-as.numeric(match(val,rn))

  }else
  {
    miss<-val
  }

  if(length(miss))
  {
    eq.nw=ob@snp.eq[-miss]
    u1<-unique(eq.nw)
    cls<-setdiff(unique(ob@snp.eq),u1)

    if(length(cls)) ## change found in equivalence class
    {
      ob@snp.eq<-fn.hash(eq.nw)

      if(is.null(ob@eq.map)) ## for non-merged object
      {  
        nw.mat<-ob@eq.mat[[1]]
        nw.mat<-nw.mat[-cls,]
        ob@eq.mat[[1]]<-nw.mat
        
      }else 
      {
        emap=ob@eq.map
        emap2=emap[-cls,]
        dm<-numeric(0)

        for(k in 1:ncol(emap))
        {
          cid<-setdiff(unique(emap[,k]),unique(emap2[,k]))
          if(length(cid))
          { 
            nw.mat<-ob@eq.mat[[k]]
            nw.mat<-nw.mat[-cid,]
            ob@eq.mat[[k]]<-nw.mat
            emap2[,k]<-fn.hash(emap2[,k])
          }
          dm<-c(dm,nrow(ob@eq.mat[[k]]))
         
        }
       
        ob@eq.map<-emap2
        ob@dim[[2]]<-dm
      } 

    }else
    {
      ob@snp.eq<-eq.nw
    }
    
    ob@snp.df<-ob@snp.df[-miss,]
    ob@dim[[1]][1]<-nrow(ob@snp.df)
    ob@dim[[1]][2]<-max(ob@snp.eq)
     
  }else
  {
    print("No Missing Position")
  }

  return(ob)

}