R/impute_PCA.R

In imp4p: Imputation for Proteomics

impute.PCA=function (tab, conditions, ncp.max=5) {

  tab_imp=as.matrix(tab);

  new_tab=tab
  new_tab.imp=tab_imp
  new_conditions=NULL
  index=NULL
  k=1
  for (j in 1:length(levels(conditions))){
    index=c(index,which(conditions==levels(conditions)[j]))
    nb_rep=sum((conditions==levels(conditions)[j]));
    new_tab[,(k:(k+nb_rep-1))]=tab[,which(conditions==levels(conditions)[j])]
    new_tab.imp[,(k:(k+nb_rep-1))]=tab_imp[,which(conditions==levels(conditions)[j])]
    new_conditions=c(new_conditions,conditions[which(conditions==levels(conditions)[j])])
    k=k+nb_rep
  }

  tab=new_tab
  tab_imp=new_tab.imp
  conditions=new_conditions
  conditions=factor(as.character(conditions),levels=as.character(unique(conditions)));

  nb_cond=length(levels(conditions));
  nb_rep=rep(0,nb_cond);
  k=1;

  for (n in 1:nb_cond){

    nb_rep[n]=sum((conditions==levels(conditions)[n]));
    #print(nb_rep[n])
    xincomplete=as.matrix(new_tab[,(k:(k+nb_rep[n]-1))]);
    nbna=fast_apply_nb_na(xincomplete,1);
    if (sum(nbna)>0){
      xincomplete1=xincomplete[which(nbna!=nb_rep[n]),];
      nbna2=fast_apply_nb_na(xincomplete1,1);
      if (sum(nbna2)>0){
        rngseed(1234567);
        nb <- estim_ncpPCA(xincomplete1,ncp.max=ncp.max)
        xcomplete1 <- imputePCA(xincomplete1,ncp=nb$ncp)
        tab_imp[which(nbna!=nb_rep[n]),(k:(k+nb_rep[n]-1))]=xcomplete1$completeObs;
      }
    }
    #print("OK")
    k=k+nb_rep[n];

  }

  tab_imp[,index]=tab_imp
  colnames(tab_imp)=colnames(tab)

  return(tab_imp)
}