R/testProbesRGChannelSet.R

In TJGorrie/melonProbes: melonProbes

   #TestProbes RGSet (RGChannelSet)

   setMethod(f= "testProbes",
            signature(betas="RGChannelSet"),
            definition=function(betas,manifest = c('450k', 'EPIC'), beadcounts = NULL, 
                              detection = NULL, nb = .2, np = .2, nvar = .5, ot,
                              nbCount = 3, nbThresh = 0.05, pvCount = 0.05, 
                              pvThresh = 0.01, nvarThresh = 0.05)
        
              { betasP <- preprocessRaw(betas)
            
                #betas of object
                betRG <- getBeta(betasP)
                
                #ot
                ot <- got(betasP)
                
                #beadcount
                beadcount <- NULL
                message("No beadCounts available")
                
                #detectionP
                dp <- detectionP(betas)
                
                out <-  testProbes(betas=betRG,manifest = c('450k', 'EPIC'), 
                                   beadcounts = beadcount, detection = dp, nb = nb, np = np,
                                   nvar = nvar, ot = ot,nbCount = nbCount, nbThresh = nbThresh,
                                   pvCount = pvCount, pvThresh = pvThresh, 
                                   nvarThresh = nvarThresh)  
            
                return(out)
  
                
                 }
              )