R/blineShift.R

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of  ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the    ##
## GNU General Public License for more details.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# blineShift: Shift baseline to 0
#-------------------------------------------------------------------------------

#' @name blineShift
#' @title Shift the baseline to 0
#' 
#' @description 
#' \code{blineShift} Takes in dose-response data and shifts the baseline
#' to 0 based on the window. 
#' 
#' @param resp Numeric, the response values
#' @param logc Numeric, the log10 concentration values
#' @param wndw Numeric, the threshold window 
#' 
#' @note
#' This function is not exported and is not inteded to be used by the user.
#' 
#' @keywords internal
#' 
#' @return A numeric vector containing the shifted response values
#' 
#' @seealso \code{\link{mc3_mthds}}, \code{\link{mc3}}
#' 
#' @importFrom stats median lm 

blineShift <- function(resp, logc, wndw) {

    wndw <- unique(wndw)[1]

    ordr <- order(logc)
    resp <- resp[ordr]
    logc <- logc[ordr]

    uconc <- unique(logc)
    nconc <- length(uconc)

    if (any(is.na(resp))) return(resp)
    if (nconc < 4) return(resp)

    low <- seq_len(max(ceiling(nconc/4), 2))
    rsub <- resp[which(logc %in% uconc[low])]
    csub <- logc[which(logc %in% uconc[low])]
    low_med <- median(rsub)
    m <- lm(rsub ~ csub)$coefficients["csub"]
    if (is.na(m)) m <- 0
    test1 <- abs(low_med) <= wndw
    test2 <- abs(m) <= wndw/low[length(low)]
    if (test1 & test2) resp <- resp - low_med

    resp[order(ordr)]

}

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