R/getProb.R

In isglobal-brge/MADloy: Package to detect mosaic LOY from SNP array data

#' Get probability matrix of three status (LOY, normal, XYY)
#' 
#' @param x an object of class 'LOY'
#' @return a matrix of probabilities
#' 
#' @export
#' 
#' 
getProb <- function(x) {
    n <- length(x$class)
    idx <- sapply(x$class, function(x) which(x == c("LOY", "normal", "XYY")))
    ans <- matrix(0, ncol = 3, nrow = n)
    
    for (i in 1:n) {
        if (idx[i] == 1) 
            ans[i, 1:2] <- c(1 - x$prob[i], x$prob[i])
        if (idx[i] == 2 & x$data[i] >= 0) 
            ans[i, 2:3] <- c(1 - x$prob[i], x$prob[i])
        if (idx[i] == 2 & x$data[i] < 0) 
            ans[i, 1:2] <- c(x$prob[i], 1 - x$prob[i])
        if (idx[i] == 3) 
            ans[i, 2:3] <- c(x$prob[i], 1 - x$prob[i])
    }
    colnames(ans) <- c("LOY", "normal", "XYY")
    ans
}