Nothing
getProbs.cghCall <-
function (x)
{
if (!inherits(x, "cghCall"))
stop("object must be of class 'cghCall'")
requireNamespace("Biobase", quietly = TRUE)
requireNamespace("CGHbase", quietly = TRUE)
Clone <- Biobase::featureNames(x)
Chromo <- CGHbase::chromosomes(x)
BPstart <- CGHbase::bpstart(x)
BPend <- CGHbase::bpend(x)
Calls <- CGHbase::calls(x)
Probloss <- CGHbase::probloss(x)
Probnorm <- CGHbase::probnorm(x)
Probgain <- CGHbase::probgain(x)
colnam <- c(colnames(Probloss), colnames(Probnorm), colnames(Probgain))
if (is.null(CGHbase::probamp(x))) {
allprob <- c()
ncl <- ncol(Probnorm)
for (i in 1:ncl) {
Probsall <- cbind(Probloss[, i], Probnorm[, i], Probgain[,
i])
colnames(Probsall) <- c(colnam[i], colnam[ncl + i],
colnam[2 * ncl + i])
allprob <- cbind(allprob, Probsall)
}
}
else {
Probamp <- CGHbase::probamp(x)
colnam <- c(colnam, colnames(Probamp))
allprob <- c()
ncl <- ncol(Probnorm)
for (i in 1:ncl) {
Probsall <- cbind(Probloss[, i], Probnorm[, i], Probgain[,
i], Probamp[, i])
colnames(Probsall) <- c(colnam[i], colnam[ncl + i],
colnam[2 * ncl + i], colnam[3 * ncl + i])
allprob <- cbind(allprob, Probsall)
}
}
allprob2 <- round(allprob, 3)
probs <- data.frame(Clone, Chromo, BPstart, BPend, allprob2)
probs
}
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