R/estTHOR.R

In scottwalmsley/THOR: Determines a spectral count threshold cutoff.

#' est.THOR Estimate the GQ mediated cutoff.
#'
#' @param THOR.result The thor function result. 
#'
#' @return A list containing
#' @export
#'
#' @examples
est.THOR = function(THOR.result){
  
  pv = seq(0.0001,1,0.005);
  
  est.CO = function(M,pv,id){
    cutoffs = array();	
    id = seq(1,length(M$csum),1)
    for(i in 1:(length(pv))){
      min.id = min(id[M$csum >= pv[i]]);
      cutoffs[i] = M$Ref[min.id];
      
    }
    l = loess.smooth(cutoffs,pv, span=0.5,evaluation=100);
    return(list(CO=cutoffs,pv=pv,loess = l));
  }
  
  ecd = list();
  for(N in 1:length(THOR.result)){
    ecd[[N]] = est.CO(THOR.result[[N]],pv,id); 
    
  }
  return(list(ecd=ecd));
}