R/sc2.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: Perform level 2 single-concentration processing
#-------------------------------------------------------------------------------

#' @template proclvl
#' @templateVar LVL 2
#' @templateVar type sc
#'
#' @param ae Integer of length 1, assay endpoint id (aeid) for processing.
#' @param wr Logical, whether the processed data should be written to the gtox
#' database
#'
#' @details
#' Level 2 single-concentration processing defines the bmad value, and uses the
#' activity cutoff methods from sc2_aeid and sc2_methods to make an activity
#' call.
#'
#' @seealso \code{\link{Method functions}}, \code{\link{SC2_Methods}}
#'
#' @keywords internal
#' 
#' @import data.table
#' @importFrom stats mad median

sc2 <- function(ae, wr=FALSE) {

    ## Variable-binding to pass R CMD Check
    bmad <- resp <- wllt <- tmp <- spid <- logc <- hitc <- max_med <- NULL

    owarn <- getOption("warn")
    options(warn=1)
    on.exit(options(warn=owarn))

    ## Check the ae input
    if (length(ae) > 1) {
        warning("ae must be of length 1. Level 2 processing incomplete; no ",
                "updates\n  made to the sc2 table for AEIDS ",
                paste(ae, collapse=", "), ".")
        if(wr) return(FALSE) else return(list(FALSE, NULL))
    }

    stime <- Sys.time()

    ## Load level 1 data
    dat <- gtoxLoadData(lvl=1L, type="sc", fld="aeid", val=ae)

    ## Check if any level 1 data was loaded
    if (nrow(dat) == 0) {
        warning("No level 1 data for AEID", ae,
                ". Level 2 processing incomplete;",
                " no updates\n  made to the sc2 table for AEID", ae, ".")
        if(wr) return(FALSE) else return(list(FALSE, NULL))
    }

    ttime <- round(difftime(Sys.time(), stime, units="sec"), 2)
    ttime <- paste(unclass(ttime), units(ttime))
    message("Loaded L1 AEID", ae, " (", nrow(dat),
            " rows; ", ttime,")\n", sep="")

    stime <- Sys.time()

    ## Calculate bmad
    dat[ , bmad := mad(resp[wllt == "t"])]

    ## Collapse by spid
    dat[ , tmp := median(resp), by=list(spid, wllt, logc)]
    dat[ , c("tmpi", "max_med") := list(.GRP, max(tmp)), by=spid]

    ## Initialize coff vector
    coff <- 0

    ## Load cutoff functions
    mthd_funcs <- sc2_mthds()

    ## Load cutoff methods
    ms <- gtoxMthdLoad(lvl=2L, id=ae, type="sc")
    if (nrow(ms) == 0) {
        warning("No level 5 methods for AEID", ae, " -- cutoff will be 0.")
    }

    ## Apply cutoff methods
    exprs <- lapply(mthd_funcs[ms$mthd], do.call, args=list())
    fenv <- environment()
    invisible(rapply(exprs, eval, envir=fenv))

    ## Determine final cutoff
    dat[ , coff := max(coff)]

    ## Determine hit-call
    dat[ , hitc := as.integer(max_med >= coff)]

    ttime <- round(difftime(Sys.time(), stime, units="sec"), 2)
    ttime <- paste(unclass(ttime), units(ttime))
    message("Processed L2 AEID", ae, " (", nrow(dat),
            " rows; ", ttime, ")\n", sep="")

    res <- TRUE

    outcols <- c(
        "s0id", "s1id", "spid", "aeid", "max_med",
        "bmad", "coff", "hitc", "tmpi"
    )
    dat <- dat[ , .SD, .SDcols=outcols]

    ## Load into sc2 table -- else return results
    if (wr) {
        stime <- Sys.time()
        gtoxWriteData(dat=dat, lvl=2L, type="sc")

        ttime <- round(difftime(Sys.time(), stime, units="sec"), 2)
        ttime <- paste(unclass(ttime), units(ttime))
        message("Wrote L2 AEID", ae, " (", nrow(dat),
                " rows; ", ttime, ")\n", sep="")
    } else {
        res <- c(res, list(dat))
    }

    return(res)

}
#-------------------------------------------------------------------------------