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refactored cndx and repi code #134

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Sep 6, 2023
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refactored cndx and repi code #134

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43 changes: 4 additions & 39 deletions R/mc1.R
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Original file line number Diff line number Diff line change
Expand Up @@ -56,46 +56,11 @@ mc1 <- function(ac, wr = FALSE) {
## Set conc to three significant figures
dat[ , conc := signif(conc, 3)]

## Define replicate id
# Order by the following columns
setkeyv(dat, c('acid', 'srcf', '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, srcf, apid, "rep1", conc, sep = "_")]
dat[wllt == "t" & acid %in% nconc[nconc == 1, acid],
rpid := paste(acid, spid, wllt, srcf, "rep1", conc, sep = "_")]
# Define rpid column for non-test compound wells
dat[wllt != "t",
rpid := paste(acid, spid, wllt, srcf, apid, "rep1", conc, sep = "_")]

# set repid based on rowid
dat[, dat_rpid := rowid(rpid)]
dat[, rpid := sub("_rep[0-9]+.*", "",rpid, useBytes = TRUE)]
dat[, rpid := paste0(rpid,"_rep",dat_rpid)]

## Define concentration index
indexfunc <- function(x) as.integer(rank(unique(x))[match(x, unique(x))])
dat[ , cndx := indexfunc(conc), by = list(rpid)]
# set concentration index
dat[, cndx := frank(conc, ties.method = "dense"), by = .(acid, spid, wllt, srcf, apid)]

## 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 := rowidv(trdt)]
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]
# set replicate index
dat[, repi:=rowid(conc),by= .(acid, spid, wllt, srcf, apid)]

ttime <- round(difftime(Sys.time(), stime, units = "sec"), 2)
ttime <- paste(unclass(ttime), units(ttime))
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