R/mtlr_fun2.R

In SydneyBioX/SurvBenchmark_package: survival approaches benchmarking

#' mtlr model with de for feature selection
#'
#'
#' @param r a numeric value, a seed to run this method
#' @param data a dataframe, the data used to performance this survival model
#' @param cvK a numeric value, cross-validation fold
#' @param numm a numeric value, the number of variables,i.e.for example, number of proteins in the data
#' @param topnumm a numeric value, the number of variables selected to be passed into the model, for example, the number of DE genes
#' @param timess a numeric vector of length 15, contains time points to get the time-dependent AUC values
#' @return a data.frame with allevaluation measurements in all columns and rows are each fold results from cross-validation
#'
#' @examples
#' data("exampledt", package = "SurvBenchmark")
#' fitform_ogl=survival::Surv(time,status)~.
#' formula1=fitform_ogl
#' formula2=fitform_ogl
#' formula3=survival::Surv(time,status)~1
#' formula4=survival::Surv(time,status)~1
#' form1=as.formula(~.)
#' timess=seq(as.numeric(summary(cancerdt2_1$time)[2]),as.numeric(summary(cancerdt2_1$time)[5]),(as.numeric(summary(cancerdt2_1$time)[5])-as.numeric(summary(cancerdt2_1$time)[2]))/14)

#' time1=timess[3]
#' stepnumber=10
#' penaltynumber=100
#' want=mtlr_fun2(1,cancerdt2_1,5, 16047,1000,timess);
#' @export

mtlr_fun2=function(r,data,cvK,numm,topnumm,timess){
  if (! is.numeric(r)) stop("Input seed is wrong")
  if (! is.numeric(cvK)) stop("Input cross-validation fold number is wrong")
  if (! is.numeric(numm)) stop("Input number of variables is wrong")
  if (! is.numeric(topnumm)) stop("Input number of top variable selection is wrong")
  if (is.null(dim(data))) stop("Input data is wrong")
  if (length(timess)!=15) stop("Wrong time vector length")
  if (class(timess)!= "numeric") stop("Wrong time vector type")
  set.seed(r)
  print(r)
  cvSets = cvTools::cvFolds(nrow(data), cvK)  # permute all the data, into 5 folds
  bicfun=purrr::possibly(function(j){
    test_id = cvSets$subsets[cvSets$which == j]
    test = data[test_id, ]
    train = data[-test_id, ]
    ## Limma analysis:
    protein4_1=train[,c(1:numm)]
    protein4_2=as.matrix(t(protein4_1))
    groupname <-as.factor( as.character(train$os_class))
    design <- model.matrix(~ groupname + 0)
    fit <- limma::lmFit(protein4_2, design)
    cont.matrix <- limma::makeContrasts(contrasts = "groupnamegood-groupnamepoor", levels=design)
    fit2 <- limma::contrasts.fit(fit, cont.matrix)
    fit2 <- limma::eBayes(fit2)
    tT <- limma::topTable(fit2,number = nrow(fit2))
    tT = tT %>% rownames_to_column("GeneName") %>% select(GeneName, logFC, P.Value, adj.P.Val)
    # head(tT)
    # sum(tT$P.Value<0.05)
    selectedname=tT$GeneName[1:topnumm]


    train=train[,colnames(train)%in%c(selectedname,"status","time")]
    test=test[,colnames(test)%in%c(selectedname,"status","time")]


    #fitform_ogl=as.formula(paste("Surv(time, status)~ ", paste(colnames(train)[1:(dim(train)[2]-2)], collapse= "+")))
    fitform_ogl=survival::Surv(time,status)~.
    form1=as.formula(~.)
    formula1=fitform_ogl
    formula2=fitform_ogl
    formula3=survival::Surv(time,status)~1
    formula4=survival::Surv(time,status)~1

    #form1=as.formula(paste("~ ",paste(colnames(train)[1:(dim(train)[2]-2)], collapse= "+")))

    set.seed(123)
    formula=fitform_ogl
    se=MTLR::mtlr_cv(formula,train, C1_vec = c(0.01,0.05,0.1,0.5,1,10))
    fullMod <- MTLR::mtlr(formula = formula, data = train,C1=se$best_C1)
    pred_tr <- predict(fullMod, train, type = "prob_event")
    pred_te <- predict(fullMod, test, type = "prob_event")
    #harrel cindex
    harrelC1 <- Hmisc::rcorr.cens(-pred_te,with(test,Surv(time,status)))
    hc<-harrelC1["C Index"]
    #begg cindex
    lp<- pred_tr
    lpnew <- pred_te
    Surv.rsp <- survival::Surv(train$time, train$status)
    Surv.rsp.new <- survival::Surv(test$time, test$status)
    bc <- survAUC::BeggC(Surv.rsp, Surv.rsp.new,lp, lpnew)
    #uno cindex
    unoc<-survAUC::UnoC(Surv.rsp, Surv.rsp.new, lpnew)
    #gh cindex
    ghc<-survAUC::GHCI(lpnew)
    #br
    briers1 <- survAUC::predErr(Surv.rsp, Surv.rsp.new, lp, lpnew,times=test$time, type = "brier", int.type = "unweighted")$error
    br1<-sum(na.omit(briers1))
    briers2<-survAUC::predErr(Surv.rsp, Surv.rsp.new, lp, lpnew,times=test$time, type = "brier", int.type = "weighted")$error
    br2<-sum(na.omit(briers2))
    ibsfun1=purrr::possibly(function(modell){
      briers3 <- pec::pec(list("cox1"=modell),data=test,formula=formula1,cens.model="cox")
      return(crps(briers3)[2])
    },otherwise = NA)
    #briers3 <- pec(list("cox1"=original_cox1),data=test,formula=Surv(tx_gperiod,tx_gstatus)~recip_sex+recip_eth+recip_age+recip_height+recip_weight+recip_smoker+recip_lung+recip_coronary+recip_pvd+recip_cvd+recip_diabetes+recip_waittime+donor_age+donor_sex+donor_height+donor_weight+donor_causedeath_cva+donor_dcd+donor_diabetes+donor_ht+donor_smoker+donor_creatinine+tx_ischaemia+tx_misa+tx_misb+tx_misdr,cens.model="cox")
    #bs3[j]<-crps(briers3)[2]
    br3<-ibsfun1(fullMod)
    ibsfun2=purrr::possibly(function(modell){
      briers4 <- pec::pec(list("cox1"=modell),data=test,formula=formula2,cens.model="marginal")
      return(crps(briers4)[2])
    },otherwise = NA)
    br4<-ibsfun2(fullMod)
    ibsfun3=purrr::possibly(function(modell){
      briers5 <- pec::pec(list("cox1"=modell),data=test,formula=formula3,cens.model="cox")
      return(crps(briers5)[2])
    },otherwise = NA)
    br5<-ibsfun3(fullMod)
    ibsfun4=purrr::possibly(function(modell){
      briers6 <- pec::pec(list("cox1"=modell),data=test,formula=formula4,cens.model="marginal")
      return(crps(briers6)[2])
    },otherwise = NA)
    br6<-ibsfun4(fullMod)
    #time-dependent auc
    times <- timess
    AUC_CD <- survAUC::AUC.uno(Surv.rsp, Surv.rsp.new, lpnew, times)
    a1=AUC_CD$auc[1]
    a2=AUC_CD$auc[2]
    a3=AUC_CD$auc[3]
    a4=AUC_CD$auc[4]
    a5=AUC_CD$auc[5]
    a6=AUC_CD$auc[6]
    a7=AUC_CD$auc[7]
    a8=AUC_CD$auc[8]
    a9=AUC_CD$auc[9]
    a10=AUC_CD$auc[10]
    a11=AUC_CD$auc[11]
    a12=AUC_CD$auc[12]
    a13=AUC_CD$auc[13]
    a14=AUC_CD$auc[14]
    a15=AUC_CD$auc[15]
    a=AUC_CD$iauc
    return(c(hc,bc,unoc,ghc,br1,br2,br3,br4,br5,br6,a1,a2,a3,a4,a5,a6,a7,a8,a9,a10,a11,a12,a13,a14,a15,a))},otherwise=NA)

  cv5_result=rbind.data.frame(bicfun(1),bicfun(2),bicfun(3),bicfun(4),bicfun(5))
  #colnames(cv5_result)=c("hc","bc","unoc","ghc","br1","br2","br3","br4","br5","br6","a1","a2","a3","a4","a5","a6","a7","a8","a9","a10","a11","a12","a13","a14","a15","a")

  # want=cbind.data.frame(hc_acc5,bc_acc5,unoc_acc5,ghc_acc5,bs1,bs2,bs3,bs4,bs5,bs6,auc1,auc2,auc3,auc4,auc5,auc6,auc7,auc8,auc9,auc10,auc11,auc12,auc13,auc14,auc15,auc)
  return(cv5_result)}