R/rbp.beta.predict.R

In chaolinzhanglab/splicescope: Splicescope

#' predict neuronal maturation with all module exons using beta regression methods with RBP specif exons
#'
#' @param data processed splicing matrix with 'NA' and extreme value removed
#'
#' @return data.frame with Predicated maturation stage and Predication confidence score
#' @export
#'
#' @examples
rbp.beta.predict <- function(data, devcortex.rbp) {
    library(betareg)
    res <- data.frame(matrix("", ncol = 2, nrow = ncol(data)), stringsAsFactors = F)
    rownames(res) <- colnames(data)
    colnames(res) <- c("Maturation", "ConfidenceScore")
    
    for (i in 1:ncol(data)) {
        if(max(data[,i])-min(data[,i])>0){
          beta.res <- betareg(data[, i] ~ ., as.data.frame(devcortex.rbp))
          beta.Sdis <- get.dis.rbp(beta.res, devcortex.rbp)
          knn.res <- knn.flex.reg(beta.Sdis, 1)
          confi.score <- 1 - min(beta.Sdis)/max(beta.Sdis)
          beta.class <- unlist(sapply(knn.res, function(x) return(Score[[x]])))
          res[i, 1] <- beta.class
          res[i, 2] <- confi.score
        }else{
          res[i, 1] <- NA
          res[i, 2] <- NA
        }
        
        
    }
    
    res
    
}