R/sc2_mthds.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.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# sc2_mthds: Load list of sc2 method functions
#-------------------------------------------------------------------------------

#' @name SC2_Methods
#' @title List of level 2 single-concentration hit-call functions
#'
#' @description
#' \code{sc2_mthds} returns a list of functions to be used during level 2
#' single-concentration processing.
#'
#' @return A list functions
#'
#' @seealso \code{\link{sc2}}, \code{\link{Method functions}} to query what
#' methods get applied to each acid
#'
#' @details
#' The functions contained in the list returned by \code{sc2_mthds} return
#' a list of expressions to be executed in the \code{sc2} (not exported)
#' function environment. The functions are described here for reference
#' purposes, The \code{sc2_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 single-concentration processing is
#' available in the package vignette, "Pipeline_Overview."
#'
#' \describe{
#'   \item{bmad3}{Add a cutoff value of 3*bmad.}
#'   \item{pc20}{Add a cutoff value of 20.}
#'   \item{log2_1.2}{Add a cutoff value of log2(1.2).}
#'   \item{log10_1.2}{Add a cutoff value of log10(1.2).}
#'   \item{bmad5}{Add a cutoff value of 5*bmad.}
#'   \item{bmad6}{Add a cutoff value of 6*bmad.}
#'   \item{bmad10}{Add a cutoff value of 10*bmad.}
#'   \item{pc30orbmad3}{Add a cutoff value of either 30 or 3*bmad, whichever
#'   is less.}
#' }
#'
#' @keywords internal
#' 
#' @note
#' This function is not exported and is not intended to be used by the user.


sc2_mthds <- function() {

    list(

        bmad3=function() {

            e1 <- bquote(coff <- c(coff, dat[ , unique(bmad)*3]))
            list(e1)

        },

        pc20=function() {

            e1 <- bquote(coff <- c(coff, 20))
            list(e1)

        },

        log2_1.2=function() {

            e1 <- bquote(coff <- c(coff, log2(1.2)))
            list(e1)

        },

        log10_1.2=function() {

            e1 <- bquote(coff <- c(coff, log10(1.2)))
            list(e1)

        },

        bmad5=function() {

            e1 <- bquote(coff <- c(coff, dat[ , unique(bmad)*5]))
            list(e1)

        },

        bmad6=function() {

            e1 <- bquote(coff <- c(coff, dat[ , unique(bmad)*6]))
            list(e1)

        },

        bmad10=function() {

            e1 <- bquote(coff <- c(coff, dat[ , unique(bmad)*10]))
            list(e1)

        },

        pc30orbmad3=function() {

            e1 <- bquote(coff <- c(coff, dat[ , min(30, unique(bmad)*3)]))
            list(e1)

        },

        pc0.88=function() {

            e1 <- bquote(coff <- c(coff, 20))
            list(e1)

        },

        log2_1.5=function() {

            e1 <- bquote(coff <- c(coff, log2(1.5)))
            list(e1)

        }

    )
}

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