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PeakML.Isotope.getAbunMtxList <- function(isotopeChroms, sampleGroups, useArea){
# PRE:
# isotopeChroms <- the chrom data for isotopes see. PeakML.Isotope.getChromData
# sampleGroup <- the sample groups
# useArea -> TRUE will sum up all intensities to give area under the curve, FALSE gives maximum intensities
# POST:
# Generates matrix containing the relative abundance of labelled vs unlabelled isotopes based on the the mean of the peaks in each groups
getAbunMtx <- function(abunList, sampleGroups, numCarbons){
cat("sampleGroups : ", sampleGroups, "\n")
abunMtx <- matrix(nrow = length(sampleGroups), ncol = numCarbons)
#row.names(abunMtx) <- sampleGroups
names(abunMtx) <- c("AI", 1:(numCarbons-1))
for (sg in 1:length(sampleGroups)){
maxSignals <- unlist(abunList[[sg]][[1]])
for (itop in 2:numCarbons){
numReplicates <- length(abunList[[sg]][[itop]])
sigAbunts <- vector()
labIntesity <- vector()
for (repl in 1:numReplicates){
if (!is.null(abunList[[sg]][[itop]][[repl]])){
if (!is.null(abunList[[sg]][[1]][[repl]])){
sigAbunts[repl] <- abunList[[sg]][[itop]][[repl]] / abunList[[sg]][[1]][[repl]]
} else{
labIntesity <- c(labIntesity, abunList[[sg]][[itop]][[repl]]) # this is in case no unlabelled peaks were found
}
maxSignals <- c(maxSignals, abunList[[sg]][[itop]][[repl]])
} else{
sigAbunts[repl] <- NA
maxSignals <- c(maxSignals, NA)
}
}
meanAbunts <- mean(sigAbunts, na.rm=TRUE)
if (!is.nan(meanAbunts)){
abunMtx[sg, itop] <- round(meanAbunts, 2)
}
if (length(labIntesity)==numReplicates){
abunMtx[sg, itop] <- round(mean(labIntesity), 2)
}
}
abunMtx[sg, 1] <- round(mean(maxSignals, na.rm=TRUE), 2)
}
abunMtx
}
intList <- isotopeChroms[[2]]
abunMtxList <- vector("list", length(intList))
for (peakGroup in 1:length(intList)){
abunList <- vector("list", length(intList[[peakGroup]]))
for (sampleGroup in 1:length(intList[[peakGroup]])){
numIsotopes <- length(intList[[peakGroup]][[sampleGroup]])
abunList[[sampleGroup]] <- vector("list", numIsotopes)
for (isotop in 1:numIsotopes){
numReplicates <- length(intList[[peakGroup]][[sampleGroup]][[isotop]])
maxintensities <- rep(NA,numReplicates)
sumintensities <- rep(NA, numReplicates)
abunList[[sampleGroup]][[isotop]] <- vector("list", numReplicates)
for (replicate in 1:numReplicates){
if(!is.null(intList[[peakGroup]][[sampleGroup]][[isotop]][[replicate]])){
maxintensities[[replicate]] <- max(intList[[peakGroup]][[sampleGroup]][[isotop]][[replicate]])[1]
if (useArea==FALSE){
abunList[[sampleGroup]][[isotop]][[replicate]] <- max(intList[[peakGroup]][[sampleGroup]][[isotop]][[replicate]])
} else {
abunList[[sampleGroup]][[isotop]][[replicate]] <- sum(intList[[peakGroup]][[sampleGroup]][[isotop]][[replicate]])
sumintensities[[replicate]] <- sum(intList[[peakGroup]][[sampleGroup]][[isotop]][[replicate]])[1]
}
}
}
if (useArea==FALSE){
meanIntRep <- mean(maxintensities,na.rm=TRUE)
} else{
meanIntRep <- mean(sumintensities,na.rm=TRUE)
}
}
}
print(abunList)
abunMtxList[[peakGroup]] <- getAbunMtx(abunList, sampleGroups, numIsotopes)
}
abunMtxList
}
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