R/mc2_mthds.R

In philipmorrisintl/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.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# mc2_mthds: Load list of correction functions (to be used at level 2)
#-------------------------------------------------------------------------------

#' @name MC2_Methods
#' @title List of level 2 multiple-concentration correction functions
#'
#' @description
#' \code{mc2_mthds} returns a list of correction/transformation functions
#' to be used during level 2 multiple-concentration processing.
#'
#' @return A list functions
#'
#' @seealso \code{\link{mc2}}, \code{\link{Method functions}} to query what
#' methods get applied to each acid
#'
#' @details
#' The functions contained in the list returned by \code{mc2_mthds} return
#' a list of expressions to be executed in the \code{mc2} (not exported)
#' function environment. The functions are described here for reference
#' purposes, The \code{mc2_mthds} function is not exported, nor is it
#' intended for use.
#'
#' All available methods are described in the Available Methods section, listed
#' by the function/method name.
#'
#' @section Available Methods:
#'
#' More information about the level 2 multiple-concentration processing is
#' available in the package vignette, "Pipeline_Overview."
#'
#' \describe{
#'   \item{log2}{Take the logarithm of cval with the base 2.}
#'   \item{log10}{Take the logarithm of cval with the base 10.}
#'   \item{rmneg}{Remove entries where cval is less than 0.}
#'   \item{rmzero}{Remove entries where cval is 0.}
#'   \item{mult25}{Multiply cval by 25.}
#'   \item{mult100}{Multiply cval by 100.}
#'   \item{negshift}{Shift cval by subtracting out the minimum of cval and
#'   adding 1, such that the new minimum of cval is 1.}
#'   \item{mult25}{Multiply cval by 2.5.}
#'   \item{mult3}{Multiply cval by 3.}
#'   \item{mult6}{Multiply cval by 6.}
#' }
#'
#' @keywords internal
#' 
#' @note
#' This function is not exported and is not intended to be used by the user.


mc2_mthds <- function() {

    list(

        log2=function() {

            e1 <- bquote(dat[ , cval := log2(cval)])
            list(e1)

        },

        log10=function() {

            e1 <- bquote(dat[ , cval := log10(cval)])
            list(e1)

        },

        rmneg=function() {

            e1 <- bquote(dat[cval < 0, c('cval', 'wllq') := list(NA_real_, 0)])
            list(e1)

        },

        rmzero=function() {

            e1 <- bquote(dat[cval == 0, c('cval', 'wllq') := list(NA_real_, 0)])
            list(e1)

        },

        mult25=function() {

            e1 <- bquote(dat[ , cval := cval * 25])
            list(e1)

        },

        mult100=function() {

            e1 <- bquote(dat[ , cval := cval * 100])
            list(e1)

        },

        negshift=function() {

            e1 <- bquote(dat[ , cval := cval - min(cval, na.rm=TRUE) + 1])
            list(e1)

        },

        mult2.5=function() {

            e1 <- bquote(dat[ , cval := cval * 2.5])
            list(e1)

        },

        mult3=function() {

            e1 <- bquote(dat[ , cval := cval * 3])
            list(e1)

        },

        mult6=function() {

            e1 <- bquote(dat[ , cval := cval * 6])
            list(e1)

        },

        sub100=function() {

            e1 <- bquote(dat[ , cval := 100 - cval])
            list(e1)

        }

    )
}

#-------------------------------------------------------------------------------