R/mc1.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.                    ##
#####################################################################

#-------------------------------------------------------------------------------
# mc1: Perform level 1 processing
#-------------------------------------------------------------------------------

#' @template proclvl
#' @templateVar LVL 1
#' @templateVar type mc
#'
#' @param ac Integer of length 1, assay component id (acid) for processing.
#' @param wr Logical, whether the processed data should be written to the gtox
#' database
#'
#' @keywords internal
#' 
#' @details
#' Level 1 processing includes defining the concentration and replicate index,
#' cndx and repi, respectively.
#'
#' @import data.table

mc1 <- function(ac, wr=FALSE) {

    ## Variable-binding to pass R CMD Check
    conc <- wllt <- acid <- apid <- spid <- n <- rpid <- NULL
    cndx <- repi <- NULL

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

    ## Check the ac input
    if (length(ac) > 1) {
        warning("ac must be of length 1. Level 1 processing incomplete; no ",
                "updates\n  made to the mc1 table for ACIDS ",
                paste(ac, collapse=", "), ".")
        if(wr) return(FALSE) else return(list(FALSE, NULL))
    }

    stime <- Sys.time()

    ## Load level 0 data
    dat <- gtoxLoadData(lvl=0L, type="mc", fld="acid", val=ac)

    ## Check if any level 0 data was loaded
    if (nrow(dat) == 0) {
        warning("No level 0 data for ACID",
                ac,
                ". Level 1 processing incomplete;",
                " no updates\n  made to the mc1 table for ACID",
                ac,
                ".")
        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 L0 ACID", ac, " (", nrow(dat),
            " rows; ", ttime,")\n", sep="")

    stime <- Sys.time()

    ## Set conc to three significant figures
    dat[ , conc := signif(conc, 3)]

    ## Define replicate id
    ## Order by the following columns
    setkeyv(dat, c('acid', 'apid', 'coli', 'rowi', 'spid', 'conc'))
    ## Define rpid column for test compound wells
    nconc <- dat[wllt == "t" ,
        list(n=lu(conc)),
        by=list(acid, apid, spid)][ , list(nconc=min(n)), by=acid]
    dat[wllt == "t" & acid %in% nconc[nconc > 1, acid],
        rpid := paste(acid, spid, wllt, apid, "rep1", conc, sep="_")]
    dat[wllt == "t" & acid %in% nconc[nconc == 1, acid],
        rpid := paste(acid, spid, wllt, "rep1", conc, sep="_")]
    ## Define rpid column for non-test compound wells
    dat[wllt != "t",
        rpid := paste(acid, spid, wllt, apid, "rep1", conc, sep="_")]
    ## Increment rpid
    dat_rpid <- dat[ , rpid]
    j=2L
    while (any(duplicated(dat_rpid))) {
        ind <- duplicated(dat_rpid)
        dat_rpid[ind] <- sub("_rep[0-9]+", paste0("_rep", j), dat_rpid[ind])
        j <- j + 1
    }
    dat[ , rpid := dat_rpid]
    rm(dat_rpid)
    ## Remove conc values from rpid
    dat[ , rpid := sub("_([^_]+)$", "", rpid, useBytes=TRUE)]

    ## Define concentration index
    indexfunc <- function(x) as.integer(rank(unique(x))[match(x, unique(x))])
    dat[ , cndx := indexfunc(conc), by=list(rpid)]

    ## Define replicate index
    ## Create temporary table containing the unique replicate ids
    trdt <- unique(dat[wllt %in% c("t", "c") , list(acid, spid, wllt, rpid)])
    trdt_rpid <- trdt[ , rpid]
    trdt[ , rpid := NULL]
    trdt[ , repi := 1]
    ## Increment repi
    while (any(duplicated(trdt))) {
        trdt[duplicated(trdt), repi := repi + 1]
    }
    trdt[ , rpid := trdt_rpid]
    rm(trdt_rpid)
    ## Map replicate index back to dat
    setkey(dat, rpid)
    setkey(trdt, rpid)
    dat[ , repi := trdt[dat, repi]]

    ## Remove rpid column
    dat[, rpid := NULL]

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

    res <- TRUE

    outcols <- c("m0id", "acid", "cndx", "repi")
    dat <- dat[ , .SD, .SDcols=outcols]

    ## Load into mc1 table -- else return results
    if (wr) {
        stime <- Sys.time()
        gtoxWriteData(dat=dat, lvl=1L, type="mc")

        ttime <- round(difftime(Sys.time(), stime, units="sec"), 2)
        ttime <- paste(unclass(ttime), units(ttime))
        message(
            "Wrote L1 ACID", ac, " (", nrow(dat),
            " rows; ", ttime, ")\n", sep=""
        )
    } else {
        res <- c(res, list(dat))
    }

    return(res)

}

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