R/getInvStatus.R

In scoreInvHap: Get inversion status in predefined regions

#' Get the inversion status of a sample
#'
#' This function estimates the inversion status of the samples using the probabilities
#' computed in \code{classifSNPs}
#'
#' @param scores Matrix of probabilities (from \code{classifSNPs})
#' @return List with the results:
#' \itemize{
#' \item{class: Vector with the most probable classification}
#' \item{certainty: Vector with the certainty of the most probable classification}
#' }
getInvStatus <- function(scores) {
    scores[scores == Inf] <- 1
    class <- factor(colnames(scores)[max.col(scores)], levels = colnames(scores))
    names(class) <- rownames(scores)
    posterior <- scores/rowSums(scores)
    certainty <- apply(posterior, 1, max, na.rm = TRUE)
    certainty[certainty == -Inf] <- 0
    return(list(class = class, certainty = certainty))
}