R/mbqnThreshold.R

In arianeschad/MBQN: Mean/Median-balanced quantile normalization

#' @name mbqnGetThreshold 
#' @title Calculates the rank invariance threshold from which on MBQN 
#' should be used instead of 'classical' QN
#' @description Calculates the rank invariance threshold from which on 
#' MBQN should be used instead of 'classical' QN
#' @param mtx Matrix with samples in columns and features in rows
#' @param meanMedian Offset function for the MBQN calculation
#' @param plot Boolean values if logistic regression curves that are 
#' used to calculate intersection point should be plotted
#' @return threshold value
#' @examples 
#' set.seed(30)
#' n <- 20
#' m <- 20
#' mtx <- matrix(rnorm(m * n), m, n)
#' mbqnGetThreshold(mtx)
#' @export
mbqnGetThreshold <- function(mtx, meanMedian="mean", plot=TRUE) {
    mbqn.mtx <- mbqn(mtx,FUN = meanMedian)
    qn.mtx <- mbqn(mtx,FUN = NULL)
    
    pvalues_mbqn <- getPvalue(mbqn.mtx, mtx)
    pvalues_qn <- getPvalue(qn.mtx, mtx)

    low_thr <- 0.0
    res  <- mbqnGetNRIfeatures(mtx, low_thr = low_thr)

    nri_df <- data.frame(res$nri)
    nri_freq <- c()
    for (row in seq_len(nrow(nri_df))){
        freq <- nri_df[row,]$Freq
        nri_freq <- c(nri_freq, freq)
    }

    # Contain RI, p value and statistic
    combined_mbqn <- data.frame(nri_freq, pvalues_mbqn)
    combined_qn <- data.frame(nri_freq, pvalues_qn)

    thr = 0.01
    mbqnGetIntersect(combined_qn, combined_mbqn, thr, plot)
}

#' @name mbqnGetIntersect 
#' @title Helper function for mbqnGetThreshold
#' @description Helper function for mbqnGetThreshold
#' @param combined_qn Data frame containing RI, p value and statistic 
#' calculated for QN
#' @param combined_mbqn Data frame containing RI, p value and statistic 
#' calculated for MBQN
#' @param threshold Significance threshold for p value of Pitman-Morgan 
#' variance test
#' @param plot Boolean values if logistic regression curves that are used 
#' to calculate intersection point should be plotted
#' @return threshold value
#' @export
mbqnGetIntersect <- function(combined_qn, combined_mbqn, threshold, plot=TRUE){
    set.seed(2)
    thr <- 0.01
    combined_qn$sign <- ifelse(combined_qn$pvalue < thr, 1, 0)
    combined_mbqn$sign <- ifelse(combined_mbqn$pvalue < thr, 1, 0)
    
    model_qn <- stats::glm(sign ~ nri_freq, data = combined_qn, 
        family = "binomial")
    model_mbqn <- stats::glm(sign ~ nri_freq, data = combined_mbqn, 
        family = "binomial")
    
    if (model_qn$rank == 1){
        print("QN: GLM model rank is 1.")
    }
    
    if (model_mbqn$rank == 1){
        print("MBQN: GLM model rank is 1.")
    }
    
    z_value_qn <- summary(model_qn)$coefficients[2,3]
    sign_value_qn <- summary(model_qn)$coefficients[2,4]
    sign_value_qn <- oneSidedTest(sign_value_qn, z_value_qn)
    
    print(paste("Sign right-tailed QN: ", round(sign_value_qn, 3)))
    
    z_value_mbqn <- summary(model_mbqn)$coefficients[2,3]
    sign_value_mbqn <- summary(model_mbqn)$coefficients[2,4]
    sign_value_mbqn <- oneSidedTest(sign_value_mbqn, z_value_mbqn)
    
    print(paste("Sign right-tailed MBQN: ", round(sign_value_mbqn, 3)))
    
    # extract fitted probabilities
    predProbs_qn = stats::predict(model_qn, type="response")
    predProbs_mbqn = stats::predict(model_mbqn, type="response")
    
    f1 <- stats::approxfun(predProbs_qn - predProbs_mbqn, 
        combined_qn$nri_freq, rule=2)
    
    # truncate to two decimal digits
    intersect <- truncateDecimals(f1(0)/100, digits=2)
    print(paste('Intersect: ',intersect))
    
    # get probability values at right end of curves
    rightEndMBQN <- unname(predProbs_mbqn[which(
        combined_mbqn$nri_freq == max(combined_mbqn$nri_freq))[1]])
    rightEndQN <- unname(predProbs_qn[which(
        combined_qn$nri_freq == max(combined_qn$nri_freq))[1]])
    
    if ((sign_value_qn < 0.01) && (rightEndQN-rightEndMBQN > 0)) { #0.001
        if (intersect == min(combined_qn$nri_freq)){
            message('QN Problem: Use MBQN for whole dataset.')
        } else {
            message(paste('QN Problem: Use MBQN. NRI-threshold =',
                intersect,'suggested.'))
        }
    }
    
    if (plot){
        ggplot2::theme_set(ggplot2::theme_minimal())
        plot_combined <- ggplot2::ggplot() +
            ggplot2::geom_point(ggplot2::aes(
                x=combined_qn$nri_freq, combined_qn$sign), 
                color="#CC6666", alpha=0.3) +
            ggplot2::geom_line(ggplot2::aes(
                x=combined_qn$nri_freq, y=predProbs_qn), color="#CC6666") +
            ggplot2::geom_point(ggplot2::aes(
                x=combined_mbqn$nri_freq, combined_mbqn$sign), 
                color="#66CC99", alpha=0.3) +
            ggplot2::geom_line(ggplot2::aes(
                x=combined_mbqn$nri_freq, y=predProbs_mbqn), color="#66CC99") +
            ggplot2::ylim(0,1) +
            ggplot2::xlim(0,100) +
            ggplot2::labs(
                x = "Frequency of RI proteins [%]",
                y = "Probability of significant p-values",
                title = paste("Threshold:", threshold, ", QN: red (", 
                    round(sign_value_qn, 3),"), 
                    MBQN: green (", round(sign_value_mbqn, 3), ")"))
        print(plot_combined)
        #ggsave(paste0("logistRegr_nriVsProbab_QNandMBQN_thresh_", threshold, 
        #".pdf"), plot = plot_combined, width=10, height=8)
    }
    intersect
}


#library(PairedData)
#' @name getPvalue 
#' @title Calculates Pitman-Morgan variance test on two matrices
#' @description Calculates Pitman-Morgan variance test on two matrices
#' @param mtx1 Matrix with samples in columns and features in rows
#' @param mtx2 Matrix with samples in columns and features in rows
#' @return Data frame with p values and statistics
#' @examples 
#' set.seed(30)
#' n <- 20
#' m <- 20
#' mtx1 <- matrix(rnorm(m * n), m, n)
#' mtx2 <- mbqn(mtx1, FUN = "mean")
#' getPvalue(mtx1, mtx2)
#' @export
getPvalue <- function(mtx1, mtx2){
    protnames <- c()
    pvalues <- c()
    statistics <- c()
    options("scipen"=100, "digits"=4)
    
    if (is.null(row.names(mtx1))){
        rownames(mtx1) <- 1:nrow(mtx1)
    }
    
    for (i in seq_len(nrow(mtx1))){
        protnames <- c(protnames, row.names(mtx1)[i])
        # Pitman-Morgan variance test for decreasing variance
        pvalues <- c(pvalues, PairedData::Var.test(mtx1[i,], 
            mtx2[i,], paired=TRUE, alternative="less")$p.value)
        statistics <- c(statistics, PairedData::Var.test(mtx1[i,], 
            mtx2[i,], paired=TRUE, alternative="less")$statistic)
    }
    
    tab <- data.frame(protein=protnames, pvalue=as.numeric(pvalues), 
        statistic=as.numeric(statistics))
    # set NA values, e.g due to no variance in one of the metrices, to 0
    tab[is.na(tab)] <- 0 
    tab
}

#' @name truncateDecimals 
#' @title Truncate float to defined number of decimal values
#' @description Truncate float to defined number of decimal values
#' @param x float
#' @param digits Number of decimal values
#' @return Truncated number
#' @examples 
#' x <- 2.567836
#' truncateDecimals(x, 3)
#' @export
truncateDecimals <- function(x, digits = 2) {
    up <- 10 ^ digits
    x <- x * up
    y <- floor(x)
    y / up
}

#' @name oneSidedTest 
#' @title Recalulate p value from two-sided to one-sided 
#' @description Recalulate p value from two-sided to one-sided 
#' @param sign_value P value from two-sided significance test
#' @param z_value Z value from two-sided significance test
#' @return P value from one sided significance test
#' @export
oneSidedTest <- function(sign_value, z_value){
    if (z_value < 0){
        sign_value <- 1 - (sign_value / 2)
    } else {
        sign_value <- sign_value / 2
    }
    sign_value
}