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PeakML.Isotope.getRatioMtxList <- function(intList, sampleGroups, useArea, metName=""){
# PRE:
# intList <- list containing intensities of isotopes
# sample Groups <- the sample groupes
# useArea <- TRUE will sum up all intensities to give area under the curve, FALSE gives maximum intensities
# metName <- name of the metabolite to give the column name of the matrix.
# POST:
# Returns the matrix for each peak group, containing the ratio of labelled vs unlabelled signals for each replicate normalized to one along the columns and isotopes along the columns.
getSignalRatioMtx <- function(abunList, sampleGroup, numCarbons, numReplicates){
abunMtx <- matrix(nrow = numReplicates, ncol = numCarbons) # +1 is for adding the rownames
rnames <- c(paste(sampleGroup, as.character(c(1:numReplicates)), sep=""))
row.names(abunMtx) <- rnames
for (itop in 2:numCarbons){
for (repl in 1:numReplicates){
if (!is.null(abunList[[1]][[repl]])){
abunMtx[repl, 1] <- abunList[[1]][[repl]]
} else{
abunMtx[repl, 1] <- 0
}
if (!is.null(abunList[[itop]][[repl]])){
abunMtx[repl, itop] <- abunList[[itop]][[repl]]# / abunList[[sampleGroup]][[1]][[repl]]
} else{
abunMtx[repl, itop] <- NA
}
}
}
abunMtx
}
ratioMtxList <- vector("list", length(intList))
for (peakGroup in 1:length(intList)){
abunList <- NULL
ratioMtx <- NULL
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]])
abunList[[sampleGroup]][[isotop]] <- vector("list", numReplicates)
for (replicate in 1:numReplicates){
if(!is.null(intList[[peakGroup]][[sampleGroup]][[isotop]][[replicate]])){
if (useArea==FALSE){
abunList[[sampleGroup]][[isotop]][[replicate]] <- max(intList[[peakGroup]][[sampleGroup]][[isotop]][[replicate]])
} else {
abunList[[sampleGroup]][[isotop]][[replicate]] <- sum(intList[[peakGroup]][[sampleGroup]][[isotop]][[replicate]])
}
}
}
}
ratioMtx <- rbind(ratioMtx, getSignalRatioMtx(abunList[[sampleGroup]], sampleGroups[[sampleGroup]], numIsotopes, numReplicates))
}
cNames <- paste(metName, as.character(c(0:(numIsotopes-1))))
colnames(ratioMtx) <- cNames
ratioMtx[is.na(ratioMtx)] <- 0
ratioMtxList[[peakGroup]] <- t(ratioMtx)
}
ratioMtxList
}
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