setMethodS3("callGenotypes", "RawAlleleBFractions", function(this, ...) {
beta <- getSignals(this)
keep <- which(is.finite(beta))
beta <- beta[keep]
data <- data.frame(total=2, fracB=beta)
data <- as.matrix(data)
data2 <- TotalFracBSnpData(data)
data3 <- callGenotypes(data2)
naValue <- NA_real_
mu <- rep(naValue, times=nbrOfLoci(this))
mu[keep] <- data3[,2]
res <- clone(this)
res$y <- mu
res <- RawGenotypeCalls(res)
res
}) # callGenotypes()
setMethodS3("normalizeTumorBoost", "RawAlleleBFractions", function(this, betaN, muN=callGenotypes(betaN), ...) {
xBetaT <- getSignals(this)
xBetaN <- getSignals(betaN)
xMuN <- getSignals(muN)
xBetaTN <- normalizeTumorBoost(betaT=xBetaT, betaN=xBetaN, muN=xMuN, ...)
betaTN <- clone(this)
betaTN$y <- xBetaTN
betaTN
})
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