R/sigCheck.R

In SigCheck: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

sigCheck <- function(expressionSet, classes, survival, signature, 
                     annotation, validationSamples, 
                     scoreMethod="PCA1", threshold=median,
                     classifierMethod=svmI, modeVal,
                     survivalLabel="Survival", timeLabel="Time",
                     plotTrainingKM=TRUE, plotValidationKM=TRUE,
                     impute=TRUE){
   
   if(class(expressionSet)=="SigCheckObject") {
      if(missing(classes)) {
         classes <- expressionSet@classes
      }
      if(missing(survival)) {
         survival <- expressionSet@survival
      }
      if(missing(signature)) {
         signature <- expressionSet@signatureLabels
      }
      if(missing(annotation)) {
         annotation <- expressionSet@annotation
      }
      if(missing(validationSamples)) {
         validationSamples <- expressionSet@validationSamples
      }
      if(missing(scoreMethod)) {
         scoreMethod <- expressionSet@survivalMethod
      }
      if(missing(threshold)) {
         threshold <- expressionSet@threshold
      }
      if(missing(classifierMethod)) {
         classifierMethod <- expressionSet@classifierMethod
      }
      if(missing(modeVal)) {
         modeVal <- expressionSet@modeVal
      }
      if(missing(survivalLabel)) {
         survivalLabel <- expressionSet@survivalLabel
      }
      if(missing(timeLabel)) {
         timeLabel <- expressionSet@timeLabel
      }
      check <- sigCheck(as(expressionSet,"ExpressionSet"), 
                        classes, survival, signature, 
                        annotation, validationSamples, 
                        scoreMethod, threshold,
                        classifierMethod, modeVal,
                        survivalLabel, timeLabel,
                        plotTrainingKM, plotValidationKM,
                        impute)
      return(check)
   }
   
   if(missing(validationSamples)) {
      validationSamples <- numeric(0)
   }
   if(missing(annotation)) {
      annotation <- ""
   }
   if(missing(survival)) {
      survival <- ""
   }
   if(missing(survivalLabel)) {
      survivalLabel <- survival
   }
   if(missing(timeLabel)) {
      timeLabel <- ""
   }
   if(missing(timeLabel)) {
      timeLabel <- "Time"
   }
   if(missing(modeVal)) {
      modeVal <- ""
   }
   
   result = as(expressionSet,"SigCheckObject")
   result@classes <- classes
   result@annotation <- annotation
   result@survival <- survival
   result@signature <- signature
   result@validationSamples <- validationSamples
   result@threshold <- threshold
   result@classifierMethod <- classifierMethod
   result@survivalLabel <- survivalLabel
   result@timeLabel <- timeLabel
   result@survivalMethod <- scoreMethod
   result@modeVal <- modeVal
   
   if(!is.character(scoreMethod)) {
      scoreMethod="user"
   }
   
   if(scoreMethod=="classifier") {
      if(missing(survival)) {
         result@survival <- ""
      } else {
         result@survival <- survival
      }
      
      result@checkType <- "Classifier"
      result <- sigCheckClassifier(result,
                                   plotTrainingKM=plotTrainingKM,
                                   plotValidationKM=plotValidationKM,
                                   impute=impute)
   } else if(scoreMethod!="classifier")  {
      if(survival=="") {
         stop("Must specify a survival label.")
      } else {
         result@survival  <- survival
         result@checkType <- "Survival"
      }
      result <- sigCheckSurvival(result,
                                 modeVal=modeVal,
                                 plotTrainingKM=plotTrainingKM,
                                 plotValidationKM=plotValidationKM,
                                 impute=impute)       
   } else {
      stop("Invalid scoreMethod: [",scoreMethod,"]")
   }
   
   result@signatureLabels <- signature
   
   return(result)
}


sigCheckAll <- function(check,
                        iterations=10, 
                        known="cancer",
                        plotResults=TRUE, ...){
   
   message('Check random signatures...')
   randomGeneOutput  <-
      sigCheckRandom(check,iterations=iterations)
   
   
   message('Check known signatures...')
   knownGenesOutput  <- 
      sigCheckKnown(check,known=known)
   
   
   if(check@checkType=="Survival" || check@survival!="") {
      nosurv <- FALSE
      toPermute <- "survival"
   } else {
      nosurv <- TRUE
      toPermute <- "categories"
   }
   toPermute = c(toPermute,"features")    
   
   message(sprintf("Check permuted: [%s]...",toPermute[1]))   
   permute1Output <- 
      sigCheckPermuted(check, toPermute=toPermute[1],
                       iterations=iterations)
   message(sprintf("Check permuted: [%s]...",toPermute[2]))   
   permute2Output <- 
      sigCheckPermuted(check, toPermute=toPermute[2],
                       iterations=iterations) 
   
   if(toPermute[1]=="survival") {
      output <- list(checkRandom=randomGeneOutput,
                     checkKnown=knownGenesOutput,
                     checkPermutedSurvival=permute1Output,
                     checkPermutedFeatures=permute2Output)
   } else {
      output <- list(checkRandom=randomGeneOutput,
                     checkKnown=knownGenesOutput,
                     checkPermutedCategories=permute1Output,
                     checkPermutedFeatures=permute2Output)        
   }
   
   if(plotResults) {
      savemfrow = par("mfrow")        
      par(mfrow=c(2,2))
      
      if(check@checkType=="Classifier") {
         sigCheckPlot(output,classifier=TRUE,...)
      }
      
      if(!nosurv) {
         sigCheckPlot(output,classifier=FALSE,...)
      }
      
      par(mfrow=savemfrow)
   }
   
   return(output)
}