R/getProbs.cghCall.R

In isglobal-brge/CNVassoc: Association analysis of CNVs and imputed SNPs incorporating uncertainty

getProbs.cghCall <- function(x) {
        if (!inherits(x, "cghCall")) 
            stop("object must be of class 'cghCall'")
        
        # if (require('Biobase'))
        if (requireNamespace("Biobase", quietly = TRUE)) 
            Clone <- Biobase::featureNames(x) 
        else 
            stop("Biobase is not available")
        
        if (requireNamespace("CGHbase", quietly = TRUE)) {
            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)
            Probamp <- CGHbase::probamp(x)
        } else stop("CGHbase is not available")
        
        colnam <- c(colnames(Probloss), colnames(Probnorm), 
            colnames(Probgain))
        if (is.null(Probamp)) {
            allprob <- c()
            ncl <- ncol(Probnorm)
            for (i in seq_len(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 {
            colnam <- c(colnam, colnames(Probamp))
            allprob <- c()
            ncl <- ncol(Probnorm)
            for (i in seq_len(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
}