Nothing
#####################################################################
## 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)
}
#-------------------------------------------------------------------------------
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