R/util.R
In chkohler/IsoCorrectoR: Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experiments
Defines functions
writeCorrectionResultsToFile
defineOutputFilenames
convert2matrix
convertEnrichmentList2matrix
readFileByExt
checkElementDataLogic
checkElementDataStructure
checkMoleculeDataLogic
checkMoleculeDataStructure
checkRawDataMoleculeNames
checkRawData
errorHandler
writeLog
checkIsoCorrectionParameters
# Supporting functions
#' @importFrom methods is
#' @importFrom stringr str_c
#' @importFrom stringr str_detect
#' @importFrom readxl read_excel
#' @importFrom readr read_csv
#' @importFrom tools file_ext
#'
# Function to check parameters of IsoCorrection() function call
checkIsoCorrectionParameters <- function(MeasurementFile, ElementFile, MoleculeFile, CorrectTracerImpurity, CorrectTracerElementCore, CalculateMeanEnrichment, UltraHighRes, FileOut, FileOutFormat, ReturnResultsObject, CorrectAlsoMonoisotopic, CalculationThreshold, CalculationThreshold_UHR, logEnvironment, Testmode, verbose) {
# Check filenames
filenames <- list()
filenames[["MoleculeFile"]] <- MoleculeFile
filenames[["ElementFile"]] <- ElementFile
filenames[["MeasurementFile"]] <- MeasurementFile
filenames[["FileOut"]] <- FileOut
for (name in names(filenames)) {
if (is.na(filenames[[name]]) || filenames[[name]] == "") {
notification <- paste0("No or unsuitable value provided for parameter ", name, ".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Check boolean values
booleans <- list()
booleans[["CorrectTracerImpurity"]] <- CorrectTracerImpurity
booleans[["CorrectTracerElementCore"]] <- CorrectTracerElementCore
booleans[["CorrectAlsoMonoisotopic"]] <- CorrectAlsoMonoisotopic
booleans[["UltraHighRes"]] <- UltraHighRes
booleans[["CalculateMeanEnrichment"]] <- CalculateMeanEnrichment
booleans[["ReturnResultsObject"]] <- ReturnResultsObject
booleans[["Testmode"]] <- Testmode
for (name in names(booleans)) {
if (is.na(booleans[[name]]) || (!(booleans[[name]] == TRUE) && !(booleans[[name]] == FALSE) && !(booleans[[name]] == 0) && !(booleans[[name]] == 1))) {
notification <- paste0("No or unsuitable value provided for parameter ", name, ".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Check format of output file
isValid<-FileOutFormat%in%c("xls","csv")
if(!isValid){
notification <- paste0("The output format for the result file should be either \"xls\" or \"csv\". Yours was \"", FileOutFormat, "\".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Check CalculationThreshold values
if (!UltraHighRes) {
if (CalculationThreshold > (10^-2) || CalculationThreshold < 0) {
notification <- paste0("Input parameter 'CalculationThreshold' must be between 0 and 0.01 in normal resolution correction. If unsure, use the default value of 10^-8.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
} else if (UltraHighRes) {
if (CalculationThreshold_UHR < 0 || (CalculationThreshold_UHR != round(CalculationThreshold_UHR))) {
notification <- paste0("Input parameter 'CalculationThreshold_UHR' must be integer and non-negative in ultra high resolution correction. If unsure, use the default value of 8.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
# Function to write paths/filenames, correction parameters and errors/warnings to a log file
writeLog <- function(logEnvironment) {
logFile <- file.path(logEnvironment$param$OutputDirectory, logEnvironment$param$LogfileName)
disclaimer <- "IsoCorrectoR is free software and comes without any warranty."
write(paste0("ISOCORRECTOR LOG-FILE - ", logEnvironment$param$Timestamp, "\nIsoCorrectoR-version: ", logEnvironment$param$version, "\n\n", disclaimer,
"\n"), file = logFile)
# ERRORS AND WARNINGS
if (length(logEnvironment$error) > 0) {
write(paste0("AN ERROR HAS OCCURED, THE CORRECTION PROCESS WAS ABORTED. ERROR:\n\n", paste(logEnvironment$error, collapse = "\nError in function: "),
"\n"), file = logFile, append = TRUE)
}
if (length(logEnvironment$warning) > 0) {
write(paste0("WARNINGS HAVE OCCURRED, THE CORRECTION MAY BE FAULTY. WARNING(s):\n\n", paste(logEnvironment$warning, collapse = "\n\n"), "\n"), file = logFile,
append = TRUE)
}
# FILES AND DIRECTORIES
write(paste0("FILES AND DIRECTORIES\n\nMeasurement File: ", logEnvironment$param$MeasurementFile, "\nMolecule File: ", logEnvironment$param$MoleculeFile,
"\nElement File: ", logEnvironment$param$ElementFile, "\nWorking Directory: ", logEnvironment$param$WorkingDirectory, "\nOutput Directory: ", logEnvironment$param$OutputDirectory,
"\nResult File(s): ", logEnvironment$param$FileOut, "\n"), file = logFile, append = TRUE)
# PARAMETERS
write(paste0("PARAMETERS\n\nCorrection for tracer impurity: ", logEnvironment$param$CorrectTracerImpurity, "\nCorrection of tracer element in core molecule: ",
logEnvironment$param$CorrectTracerElementCore, "\nUltra-High-Resolution correction mode: ", logEnvironment$param$UltraHighRes, "\nCalculation of mean enrichment: ",
logEnvironment$param$CalculateMeanEnrichment, "\nMolecules in the correction process: ", paste(logEnvironment$param$molecules, collapse = ", "), "\nTracer(s): ",
paste(names(logEnvironment$param$tracers), collapse = ", "), "\nTracer purity: ", paste(logEnvironment$param$tracers, collapse = ", "), "\nLimit value for calculation: ",
logEnvironment$param$threshold, "\n"), file = logFile, append = TRUE)
}
# Function that is called in the case of anticipated exceptions or warnings for a clean exit and logging of warnings
errorHandler <- function(notification, logEnvironment, type, verbose) {
if (type == "warning" || type == "general") {
logEnvironment[[type]] <- c(logEnvironment[[type]], notification)
if (type == "warning") {
warning(notification)
} else if (type == "general") {
if(verbose){message(date(), " ", notification)}
}
} else if (type == "error") {
stop(notification)
} else {
notification <- paste0("Invalid error-type ", type, " supplied to errorHandler function")
stop(notification)
}
}
# Function to check the structure of measurement data
checkRawData <- function(inputFile, logEnvironment, verbose) {
if(verbose){message(date(), " :: checking raw data ...")}
location <- "In measurement data file: "
data <- as.data.frame(readFileByExt(inputFile, verbose=verbose))
if (ncol(data) < 2) {
notification <- paste0(location, ncol(data), " columns detected but at least 2 are required.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
if (nrow(data) < 2) {
notification <- paste0(location, nrow(data), " rows of measurements detected but at least 2 are required.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
if (names(data[1]) != "Measurements/Samples") {
notification <- paste0(location, "Entry in column 1, row 1 must be 'Measurements/Samples'.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
duplicateRow <- anyDuplicated(data[[1]])
if (duplicateRow) {
notification <- paste0(location, "Duplicate measurement identifier in row ", duplicateRow, " of column 1.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
duplicateCol <- anyDuplicated(colnames(data))
if (duplicateCol) {
notification <- paste0(location, "Duplicate sample name in column ", duplicateCol, ".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
rawDataMoleculeNames <- as.character(data[, 1])
checkRes <- checkRawDataMoleculeNames(rawDataMoleculeNames, splitString = "_")
MoleculesFound <- checkRes$moleculesFound
NoMoleculeSyntax <- checkRes$invalidMolecules
# there are some invalid molecules
if (length(NoMoleculeSyntax) != 0) {
notification <- stringr::str_c(location, paste0(length(NoMoleculeSyntax), " measurement identifiers in column 1 of the measurement data did not show proper syntax (name of molecule followed by _): ",
paste0(NoMoleculeSyntax, collapse = ", ")))
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
for (col in 2:ncol(data)) {
#if (is.element(FALSE, sapply(data[[col]], function(x) (is.numeric(x) || is.na(x))))) {
if (is.element(FALSE, vapply(data[[col]], function(x) (is.numeric(x) || is.na(x)),TRUE))) {
notification <- stringr::str_c(location, "Invalid value (not numeric and not NA) in column ", col, " of measurement file.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
MoleculesFound <- unique(MoleculesFound)
if(verbose){message(date(), " :: checking raw data [OK]\n")}
return(list(RawData = data, MoleculesFound = MoleculesFound))
}
checkRawDataMoleculeNames <- function(moleculeNames, splitString) {
tmp.split <- strsplit(moleculeNames, split = splitString)
wrongSyntax.index <- which(lapply(tmp.split, function(x) length(x) == 1) == TRUE) #no split
if (length(wrongSyntax.index) != 0) {
tmp.split <- tmp.split[-wrongSyntax.index]
}
return(list(moleculesFound = unlist(lapply(lapply(tmp.split, function(x) x[seq_len(length(x) - 1)]), function(x) if (length(x) == 1) {
x
} else {
paste0(x, collapse = splitString)
})), invalidMolecules = moleculeNames[wrongSyntax.index]))
}
# Function to check the structure of the supplied molecule file
checkMoleculeDataStructure <- function(data, logEnvironment, verbose) {
if(verbose){message(date(), " :: checking molecule data structure ...")}
# Check number of columns
if (ncol(data) != 3) {
notification <- paste0(ncol(data), " columns detected in Molecule File but 3 are required.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Check column names
colnamesMoleculeFileExp <- c("molecule", "ms ion or ms/ms product ion", "ms/ms neutral loss")
colnamesMoleculeFile <- tolower(colnames(data))
for (col in seq_len(ncol(data))) {
if (colnamesMoleculeFileExp[col] != colnamesMoleculeFile[col]) {
notification <- paste0("Column names '", paste0(colnamesMoleculeFile, collapse = ", "), "' found in the molecule file do not match those expected for the file: '",
paste0(colnamesMoleculeFileExp, collapse = ", "), "'.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Check if there are rows
if (nrow(data) == 0) {
notification <- "No rows found in molecule file."
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Use regular expressions to check column data
moleculeRegex <- "^((|Lab)[A-Z][a-z]?[1-9][0-9]*)+$"
invalidSyntax <- " doesn't match the required syntax."
for (row in seq_len(nrow(data))) {
moleculeName <- data[[1]][[row]]
# Check if Molecule names are NA
if (is.na(moleculeName)) {
notification <- paste0("In molecule file row ", row, ": No molecule name specified.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
productIon <- data[[2]][[row]]
neutralLoss <- data[[3]][[row]]
substr1 <- "In molecule file column "
substr2 <- paste0(", row ", row, ", molecule ", moleculeName, ": Molecule formula ")
locationSpecifierProduct <- paste0(substr1, "2", substr2)
locationSpecifierNeutral <- paste0(substr1, "3", substr2)
if (is.na(productIon) == FALSE && is.na(neutralLoss) == FALSE) {
if (stringr::str_detect(productIon, moleculeRegex) == FALSE) {
notification <- paste0(locationSpecifierProduct, productIon, invalidSyntax)
errorHandler(notification, logEnvironment, "error", verbose=verbose)
} else if (stringr::str_detect(neutralLoss, moleculeRegex) == FALSE) {
notification <- paste0(locationSpecifierNeutral, neutralLoss, invalidSyntax)
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
} else if (is.na(productIon) == FALSE) {
if (stringr::str_detect(productIon, moleculeRegex) == FALSE) {
notification <- paste0(locationSpecifierProduct, productIon, invalidSyntax)
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
} else {
notification <- paste0(locationSpecifierProduct, "for ", colnamesMoleculeFileExp[2], " must be provided.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
duplicate <- anyDuplicated(data[[1]])
if (duplicate != 0) {
notification <- paste0("In molecule file: Molecule ", data[[1]][duplicate], " present in duplicate.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
if(verbose){message(date(), " :: checking molecule data structure [OK]\n")}
return(data.frame(data))
}
# Check if molecule data makes sense
checkMoleculeDataLogic <- function(extractedData, UltraHighRes, CorrectTracerImpurity, ElementList, logEnvironment, verbose) {
if(verbose){message(date(), " :: :: checking molecule data logic ...")}
molecules <- names(extractedData)
numberFragments <- list()
tracers <- list()
for (molecule in molecules) {
numberFragments[[molecule]] <- sum(stringr::str_detect(names(extractedData[[molecule]]), "Fragment"))
tracers[[molecule]] <- c()
tracers[[molecule]][1] <- length(extractedData[[molecule]]$Fragment_1$Tracer)
if (numberFragments[[molecule]] > 1) {
tracers[[molecule]][2] <- length(extractedData[[molecule]]$Fragment_2$Tracer)
} else {
tracers[[molecule]][2] <- 0
}
if (sum(tracers[[molecule]]) == 0) {
notification <- paste0("In molecule file: No tracer element provided for molecule ", molecule, ".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
if (UltraHighRes == TRUE) {
for (molecule in molecules) {
if (numberFragments[[molecule]] != 1) {
notification <- paste0("In molecule file: More than one fragment provided for molecule ", molecule, ", but ultra high resolution correction is not compatible with MS/MS data.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
} else {
for (molecule in molecules) {
if ((tracers[[molecule]][1] > 1) || (tracers[[molecule]][2] > 1)) {
notification <- paste0("In molecule file: More than one tracer element provided for ms ion/product Ion and/or neutral loss of molecule ", molecule, ", but normal resolution correction is only compatible with a single tracer element.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
if ((tracers[[molecule]][1] > 0) && (tracers[[molecule]][2] > 0)) {
if (extractedData[[molecule]]$Fragment_1$IDTracer != extractedData[[molecule]]$Fragment_2$IDTracer) {
notification <- paste0("In molecule file: Tracer elements in product ion and neutral loss of molecule ", molecule, " do not match.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
}
# Check for duplicate elements in the molecule formula
for (molecule in molecules) {
duplicatesPresent <- 0
for (fragmentNo in seq_len(numberFragments[[molecule]])) {
fragment <- paste0("Fragment_", fragmentNo)
duplicatesPresent <- duplicatesPresent + anyDuplicated(names(extractedData[[molecule]][[fragment]]$Element)) + anyDuplicated(names(extractedData[[molecule]][[fragment]]$Tracer))
}
if (duplicatesPresent) {
notification <- paste0("In molecule file: Molecule ", molecule, " contains duplicate elements.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
elementsProvided <- names(ElementList)
for (molecule in molecules) {
for (fragmentNo in seq_len(numberFragments[[molecule]])) {
fragment <- paste0("Fragment_", fragmentNo)
elementsFragment <- extractedData[[molecule]][[fragment]]$Element
if (fragmentNo == 1) {
fragmentString = "ms ion/product ion"
} else {
fragmentString = "neutral loss"
}
commonString <- paste0("In molecule file: In ", fragmentString, " of molecule ", molecule, ": ")
# Check if elements in the molecule formula are present in the element file
if (anyNA(match(names(elementsFragment), elementsProvided))) {
notification <- paste0(commonString, "One or more elements in the provided formula were not found in the element file.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Do this only if the fragment contains a tracer
if (tracers[[molecule]][[fragmentNo]] > 0) {
tracersFragment <- extractedData[[molecule]][[fragment]]$Tracer
# Check if tracer elements in the molecule formula are also present as non-tracer elements (which gives the total number of atoms, not just the tracer
# atoms)
if (anyNA(match(names(tracersFragment), names(elementsFragment)))) {
notification <- paste0(commonString, "Information on total atom count (labelled + unlabelled) missing for tracer element(s).")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# For each tracer element found in the molecule formula, check the number of tracer atoms exceeds the total number of atoms of that element
for (tracer in names(tracersFragment)) {
if (tracersFragment[[tracer]] > elementsFragment[[tracer]]) {
notification <- paste0(commonString, "Number of tracer isotopes of element ", tracer, " exceeds number of atoms of that element present in total.")
errorHandler(notification, logEnvironment, "error")
}
# For each tracer element, check if a mass shift is provided in the element file
TracerMassShift <- ElementList[[tracer]]$Tracer.isotope.mass.shift
if (TracerMassShift == 0) {
notification <- paste0(commonString, "No mass shift information for tracer element ", tracer, " provided in element file.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Given correction for tracer impurity is active, for each tracer element, check if purity is provided in the element file
if (CorrectTracerImpurity == TRUE) {
for (tracer in names(tracersFragment)) {
if (ElementList[[tracer]]$Tracer.purity == 0) {
notification <- paste0(commonString, "No tracer purity information for tracer element ", tracer, " provided in element file, but correction for tracer impurity is active.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
}
}
}
if(verbose){message(date(), " :: :: checking molecule data logic [OK]")}
}
checkElementDataStructure <- function(data, logEnvironment, verbose) {
if(verbose){message(date(), " :: checking element data structure ...")}
# Check number of columns
if (ncol(data) != 4) {
notification <- paste0(ncol(data), " columns detected in Element File but 4 are required.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Check column names
colnamesElementFileExp <- c("element", "isotope abundance_mass shift", "tracer isotope mass shift", "tracer purity")
colnamesElementFile <- tolower(colnames(data))
for (col in seq_len(ncol(data))) {
if (colnamesElementFileExp[col] != colnamesElementFile[col]) {
notification <- paste0("Column names '", paste0(colnamesElementFile, collapse = ", "), "' found in the element file do not match those expected for the file: '",
paste0(colnamesElementFileExp, collapse = ", "), "'.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Check if there are rows
if (nrow(data) == 0) {
notification <- "No rows found in element file."
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Use regular expressions to check column data
regexVector <- c()
regexVector[1] <- "^[A-Z][a-z]?$"
regexVector[2] <- "(((^1|^1\\.[0]+|^[0]\\.[0-9]+)_(|-)[0-9])(/((1|1\\.[0]+|[0]\\.[0-9]+)_(|-)[0-9]))*)$"
regexVector[3] <- "^(|-)[1-9]$"
regexVector[4] <- "^1$|^1\\.[0]+$|^[0]\\.[0-9]+$"
notificationVector <- c()
notificationVector[1] <- " is no valid element symbol."
notificationVector[2] <- " doesn't show appropriate isotope abundance/mass shift definition syntax."
notificationVector[3] <- " is no valid tracer isotope mass shift definition."
notificationVector[4] <- " is no valid tracer purity definition."
for (col in seq_len(ncol(data))) {
currentCol <- data[[col]]
# This conversion of NA to empty string for columns 1 and 2 is done because NA values in columns 3 and 4 must not throw an error
for (row in seq_len(nrow(data))) {
if (is.na(currentCol[row]) && col == (1 || 2)) {
currentCol[row] <- ""
}
if (is.na(currentCol[row]) == FALSE) {
if (stringr::str_detect(currentCol[row], regexVector[col]) == FALSE) {
locationSpecifier <- paste0("In element file column ", col, ", row ", row, ": ")
notification <- paste0(locationSpecifier, currentCol[row], notificationVector[col])
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
}
# Check for duplicate elements
duplicate <- anyDuplicated(data[[1]])
if (duplicate != 0) {
notification <- paste0("In element file: Element ", data[[1]][duplicate], " present in duplicate.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
if(verbose){message(date(), " :: checking element data structure [OK]\n")}
return(data.frame(data))
}
# Check if element data makes sense
checkElementDataLogic <- function(extractedData, UltraHighRes, logEnvironment, verbose) {
#if(verbose){message(date(), " [checkElementDataLogic]")}
if(verbose){message(date(), " :: :: checking element data logic ...")}
for (element in names(extractedData)) {
if (any(duplicated(as.data.frame(extractedData[[element]]$Isotopes)$MassShift))) {
notification <- paste0("In element file: Duplicated MassShift for element ", element, ".")
errorHandler(notification, logEnvironment, "error")
}
# Without rounding, Si doesn't work as the sum is 1.000001. Howver, should we really round here?
if (round(sum(data.frame(extractedData[[element]][["Isotopes"]])[, 1]), 5) > 1) {
notification <- paste0("In element file: Sum of isotope abundances of element ", element, " is > 1.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# In case of UHR mode, check if the mass shift of the tracers is also found in the tracer elements natural isotopes. If not, probabilities cannot be
# calculated
if (UltraHighRes) {
for (element in names(extractedData)) {
TracerMassShift <- extractedData[[element]]$Tracer.isotope.mass.shift
if (TracerMassShift > 0 && is.na(match(TracerMassShift, as.data.frame(extractedData[[element]]$Isotopes)$MassShift))) {
notification <- paste0("In element file: Mass shift '", TracerMassShift, "' of tracer element ", element, " is not found in the natural isotope information of that element.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
if(verbose){message(date(), " :: :: checking element data logic [OK]")}
}
readFileByExt <- function(file, verbose) {
fileExt <- tools::file_ext(file)
if (fileExt == "") {
stop(date(), " :: no file extension for file: ", file, "\n")
} else {
if(verbose){message(date(), " :: :: detected file format: ", fileExt)}
if (fileExt %in% c("xls", "xlsx")) {
fileData <- readxl::read_excel(file)
} else if (fileExt == "csv") {
fileData <- readr::read_csv(file)
} else {
stop(date(), " :: unsupported file format: ", fileExt, "\n")
}
}
return(fileData)
}
convertEnrichmentList2matrix <- function(input, verbose) {
if(verbose){message(date(), " :: :: converting enrichment results into a matrix ...")}
# matrix with sampleIds as columns and mean enrichment for molecule on row
m <- matrix(ncol = length(input), nrow = length(input[[1]]))
colnames(m) <- names(input)
rownames(m) <- names(input[[1]])
# TODO: quick and dirty loop. find more elegant solution !!
for (i in seq_len(length(input))) {
for (i2 in seq_len(length(input[[i]]))) {
m[i2, i] <- as.numeric(input[[i]][[i2]])
} #i2
} #i
if(verbose){message(date(), " :: :: converting enrichment results into a matrix [OK]")}
return(m)
}
convert2matrix <- function(input) {
vec.transitions <- vector()
# we need to loop over all samples to really get all transitions
for (sample in names(input)) {
for (molecule in names(input[[sample]])) {
vec.transitions <- c(vec.transitions, names(input[[sample]][[molecule]][[1]]))
} #molecule
} #sample
transitions.unique <- unique(vec.transitions)
templateMat <- matrix(NA, ncol = length(names(input)), nrow = length(transitions.unique))
colnames(templateMat) <- names(input)
rownames(templateMat) <- transitions.unique
# now populate the four matrices
list.corrMat <- list()
for (corrMat in names(input[[1]][[1]])) {
templateMat2 <- templateMat
for (sample in names(input)) {
for (molecule in names(input[[sample]])) {
for (transition in names(input[[sample]][[molecule]][[corrMat]])) {
templateMat2[transition, sample] <- input[[sample]][[molecule]][[corrMat]][[transition]]
} #transition
} #molecule
} #sample
list.corrMat[[corrMat]] <- templateMat2
} #corrMat
return(list.corrMat)
} #convert2matrix
defineOutputFilenames <- function(logEnvironment,FileOut,FileOutFormat,
CalculateMeanEnrichment,CorrectAlsoMonoisotopic) {
#DEFINE NAMES OF OUTPUT FILES
logEnvironment$param$LogfileName <-
paste0(logEnvironment$param$NamePrefix, "_", FileOut, ".log")
CorrectedDataNamesBase <-
c("Corrected",
"CorrectedFractions",
"Residuals",
"RelativeResiduals")
if (CorrectAlsoMonoisotopic) {
CorrectedDataNamesBase <-
c(
CorrectedDataNamesBase,
"CorrectedMonoisotopic",
"CorrectedMonoisotopicFractions"
)
}
if (CalculateMeanEnrichment) {
CorrectedDataNames <-
c(CorrectedDataNamesBase, "MeanEnrichment", "RawData")
}
else {
CorrectedDataNames <- c(CorrectedDataNamesBase, "RawData")
}
if (FileOutFormat == "csv") {
CorrectedDataFileNames <-
vector(mode = "character",
length = length(CorrectedDataNames))
names(CorrectedDataFileNames) <- CorrectedDataNames
for (name in CorrectedDataNames) {
CorrectedDataFileNames[name] <-
paste0(logEnvironment$param$NamePrefix,
"_",
FileOut,
"_",
name,
".",
FileOutFormat)
}
logEnvironment$param$FileOut <-
paste0(CorrectedDataFileNames, collapse = ", ")
}
else if (FileOutFormat == "xls") {
logEnvironment$param$FileOut <-
paste0(logEnvironment$param$NamePrefix,
"_",
FileOut,
".",
FileOutFormat)
CorrectedDataFileNames <- NA
}
return(list("CorrectedDataNames" = CorrectedDataNames,
"CorrectedDataNamesBase" = CorrectedDataNamesBase,
"CorrectedDataFileNames" = CorrectedDataFileNames))
}
#WRITE CORRECTED DATA TO FILE
writeCorrectionResultsToFile <- function(CorrectedDataOutput,NamesCorrectedOutput,logEnvironment, verbose) {
if(verbose){message(date()," :: writing results to ",logEnvironment$param$FileOut," ...")}
if (logEnvironment$param$FileOutFormat == "xls") {
WriteXLS::WriteXLS(
CorrectedDataOutput,
file.path(logEnvironment$param$OutputDirectory, logEnvironment$param$FileOut),
perl = "perl",
row.names = TRUE
)
} else if (logEnvironment$param$FileOutFormat == "csv") {
for (name in NamesCorrectedOutput$CorrectedDataNames) {
utils::write.csv(
CorrectedDataOutput[[name]],
file = file.path(
logEnvironment$param$OutputDirectory,
NamesCorrectedOutput$CorrectedDataFileNames[name]
)
)
}
}
if(verbose){message(date()," :: writing results to ",logEnvironment$param$FileOut," [OK]\n")}
}
chkohler/IsoCorrectoR documentation built on July 18, 2020, 8:36 a.m.
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Defines functions writeCorrectionResultsToFile defineOutputFilenames convert2matrix convertEnrichmentList2matrix readFileByExt checkElementDataLogic checkElementDataStructure checkMoleculeDataLogic checkMoleculeDataStructure checkRawDataMoleculeNames checkRawData errorHandler writeLog checkIsoCorrectionParameters
# Supporting functions
#' @importFrom methods is
#' @importFrom stringr str_c
#' @importFrom stringr str_detect
#' @importFrom readxl read_excel
#' @importFrom readr read_csv
#' @importFrom tools file_ext
#'
# Function to check parameters of IsoCorrection() function call
checkIsoCorrectionParameters <- function(MeasurementFile, ElementFile, MoleculeFile, CorrectTracerImpurity, CorrectTracerElementCore, CalculateMeanEnrichment, UltraHighRes, FileOut, FileOutFormat, ReturnResultsObject, CorrectAlsoMonoisotopic, CalculationThreshold, CalculationThreshold_UHR, logEnvironment, Testmode, verbose) {
# Check filenames
filenames <- list()
filenames[["MoleculeFile"]] <- MoleculeFile
filenames[["ElementFile"]] <- ElementFile
filenames[["MeasurementFile"]] <- MeasurementFile
filenames[["FileOut"]] <- FileOut
for (name in names(filenames)) {
if (is.na(filenames[[name]]) || filenames[[name]] == "") {
notification <- paste0("No or unsuitable value provided for parameter ", name, ".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Check boolean values
booleans <- list()
booleans[["CorrectTracerImpurity"]] <- CorrectTracerImpurity
booleans[["CorrectTracerElementCore"]] <- CorrectTracerElementCore
booleans[["CorrectAlsoMonoisotopic"]] <- CorrectAlsoMonoisotopic
booleans[["UltraHighRes"]] <- UltraHighRes
booleans[["CalculateMeanEnrichment"]] <- CalculateMeanEnrichment
booleans[["ReturnResultsObject"]] <- ReturnResultsObject
booleans[["Testmode"]] <- Testmode
for (name in names(booleans)) {
if (is.na(booleans[[name]]) || (!(booleans[[name]] == TRUE) && !(booleans[[name]] == FALSE) && !(booleans[[name]] == 0) && !(booleans[[name]] == 1))) {
notification <- paste0("No or unsuitable value provided for parameter ", name, ".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Check format of output file
isValid<-FileOutFormat%in%c("xls","csv")
if(!isValid){
notification <- paste0("The output format for the result file should be either \"xls\" or \"csv\". Yours was \"", FileOutFormat, "\".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Check CalculationThreshold values
if (!UltraHighRes) {
if (CalculationThreshold > (10^-2) || CalculationThreshold < 0) {
notification <- paste0("Input parameter 'CalculationThreshold' must be between 0 and 0.01 in normal resolution correction. If unsure, use the default value of 10^-8.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
} else if (UltraHighRes) {
if (CalculationThreshold_UHR < 0 || (CalculationThreshold_UHR != round(CalculationThreshold_UHR))) {
notification <- paste0("Input parameter 'CalculationThreshold_UHR' must be integer and non-negative in ultra high resolution correction. If unsure, use the default value of 8.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
# Function to write paths/filenames, correction parameters and errors/warnings to a log file
writeLog <- function(logEnvironment) {
logFile <- file.path(logEnvironment$param$OutputDirectory, logEnvironment$param$LogfileName)
disclaimer <- "IsoCorrectoR is free software and comes without any warranty."
write(paste0("ISOCORRECTOR LOG-FILE - ", logEnvironment$param$Timestamp, "\nIsoCorrectoR-version: ", logEnvironment$param$version, "\n\n", disclaimer,
"\n"), file = logFile)
# ERRORS AND WARNINGS
if (length(logEnvironment$error) > 0) {
write(paste0("AN ERROR HAS OCCURED, THE CORRECTION PROCESS WAS ABORTED. ERROR:\n\n", paste(logEnvironment$error, collapse = "\nError in function: "),
"\n"), file = logFile, append = TRUE)
}
if (length(logEnvironment$warning) > 0) {
write(paste0("WARNINGS HAVE OCCURRED, THE CORRECTION MAY BE FAULTY. WARNING(s):\n\n", paste(logEnvironment$warning, collapse = "\n\n"), "\n"), file = logFile,
append = TRUE)
}
# FILES AND DIRECTORIES
write(paste0("FILES AND DIRECTORIES\n\nMeasurement File: ", logEnvironment$param$MeasurementFile, "\nMolecule File: ", logEnvironment$param$MoleculeFile,
"\nElement File: ", logEnvironment$param$ElementFile, "\nWorking Directory: ", logEnvironment$param$WorkingDirectory, "\nOutput Directory: ", logEnvironment$param$OutputDirectory,
"\nResult File(s): ", logEnvironment$param$FileOut, "\n"), file = logFile, append = TRUE)
# PARAMETERS
write(paste0("PARAMETERS\n\nCorrection for tracer impurity: ", logEnvironment$param$CorrectTracerImpurity, "\nCorrection of tracer element in core molecule: ",
logEnvironment$param$CorrectTracerElementCore, "\nUltra-High-Resolution correction mode: ", logEnvironment$param$UltraHighRes, "\nCalculation of mean enrichment: ",
logEnvironment$param$CalculateMeanEnrichment, "\nMolecules in the correction process: ", paste(logEnvironment$param$molecules, collapse = ", "), "\nTracer(s): ",
paste(names(logEnvironment$param$tracers), collapse = ", "), "\nTracer purity: ", paste(logEnvironment$param$tracers, collapse = ", "), "\nLimit value for calculation: ",
logEnvironment$param$threshold, "\n"), file = logFile, append = TRUE)
}
# Function that is called in the case of anticipated exceptions or warnings for a clean exit and logging of warnings
errorHandler <- function(notification, logEnvironment, type, verbose) {
if (type == "warning" || type == "general") {
logEnvironment[[type]] <- c(logEnvironment[[type]], notification)
if (type == "warning") {
warning(notification)
} else if (type == "general") {
if(verbose){message(date(), " ", notification)}
}
} else if (type == "error") {
stop(notification)
} else {
notification <- paste0("Invalid error-type ", type, " supplied to errorHandler function")
stop(notification)
}
}
# Function to check the structure of measurement data
checkRawData <- function(inputFile, logEnvironment, verbose) {
if(verbose){message(date(), " :: checking raw data ...")}
location <- "In measurement data file: "
data <- as.data.frame(readFileByExt(inputFile, verbose=verbose))
if (ncol(data) < 2) {
notification <- paste0(location, ncol(data), " columns detected but at least 2 are required.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
if (nrow(data) < 2) {
notification <- paste0(location, nrow(data), " rows of measurements detected but at least 2 are required.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
if (names(data[1]) != "Measurements/Samples") {
notification <- paste0(location, "Entry in column 1, row 1 must be 'Measurements/Samples'.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
duplicateRow <- anyDuplicated(data[[1]])
if (duplicateRow) {
notification <- paste0(location, "Duplicate measurement identifier in row ", duplicateRow, " of column 1.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
duplicateCol <- anyDuplicated(colnames(data))
if (duplicateCol) {
notification <- paste0(location, "Duplicate sample name in column ", duplicateCol, ".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
rawDataMoleculeNames <- as.character(data[, 1])
checkRes <- checkRawDataMoleculeNames(rawDataMoleculeNames, splitString = "_")
MoleculesFound <- checkRes$moleculesFound
NoMoleculeSyntax <- checkRes$invalidMolecules
# there are some invalid molecules
if (length(NoMoleculeSyntax) != 0) {
notification <- stringr::str_c(location, paste0(length(NoMoleculeSyntax), " measurement identifiers in column 1 of the measurement data did not show proper syntax (name of molecule followed by _): ",
paste0(NoMoleculeSyntax, collapse = ", ")))
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
for (col in 2:ncol(data)) {
#if (is.element(FALSE, sapply(data[[col]], function(x) (is.numeric(x) || is.na(x))))) {
if (is.element(FALSE, vapply(data[[col]], function(x) (is.numeric(x) || is.na(x)),TRUE))) {
notification <- stringr::str_c(location, "Invalid value (not numeric and not NA) in column ", col, " of measurement file.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
MoleculesFound <- unique(MoleculesFound)
if(verbose){message(date(), " :: checking raw data [OK]\n")}
return(list(RawData = data, MoleculesFound = MoleculesFound))
}
checkRawDataMoleculeNames <- function(moleculeNames, splitString) {
tmp.split <- strsplit(moleculeNames, split = splitString)
wrongSyntax.index <- which(lapply(tmp.split, function(x) length(x) == 1) == TRUE) #no split
if (length(wrongSyntax.index) != 0) {
tmp.split <- tmp.split[-wrongSyntax.index]
}
return(list(moleculesFound = unlist(lapply(lapply(tmp.split, function(x) x[seq_len(length(x) - 1)]), function(x) if (length(x) == 1) {
x
} else {
paste0(x, collapse = splitString)
})), invalidMolecules = moleculeNames[wrongSyntax.index]))
}
# Function to check the structure of the supplied molecule file
checkMoleculeDataStructure <- function(data, logEnvironment, verbose) {
if(verbose){message(date(), " :: checking molecule data structure ...")}
# Check number of columns
if (ncol(data) != 3) {
notification <- paste0(ncol(data), " columns detected in Molecule File but 3 are required.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Check column names
colnamesMoleculeFileExp <- c("molecule", "ms ion or ms/ms product ion", "ms/ms neutral loss")
colnamesMoleculeFile <- tolower(colnames(data))
for (col in seq_len(ncol(data))) {
if (colnamesMoleculeFileExp[col] != colnamesMoleculeFile[col]) {
notification <- paste0("Column names '", paste0(colnamesMoleculeFile, collapse = ", "), "' found in the molecule file do not match those expected for the file: '",
paste0(colnamesMoleculeFileExp, collapse = ", "), "'.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Check if there are rows
if (nrow(data) == 0) {
notification <- "No rows found in molecule file."
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Use regular expressions to check column data
moleculeRegex <- "^((|Lab)[A-Z][a-z]?[1-9][0-9]*)+$"
invalidSyntax <- " doesn't match the required syntax."
for (row in seq_len(nrow(data))) {
moleculeName <- data[[1]][[row]]
# Check if Molecule names are NA
if (is.na(moleculeName)) {
notification <- paste0("In molecule file row ", row, ": No molecule name specified.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
productIon <- data[[2]][[row]]
neutralLoss <- data[[3]][[row]]
substr1 <- "In molecule file column "
substr2 <- paste0(", row ", row, ", molecule ", moleculeName, ": Molecule formula ")
locationSpecifierProduct <- paste0(substr1, "2", substr2)
locationSpecifierNeutral <- paste0(substr1, "3", substr2)
if (is.na(productIon) == FALSE && is.na(neutralLoss) == FALSE) {
if (stringr::str_detect(productIon, moleculeRegex) == FALSE) {
notification <- paste0(locationSpecifierProduct, productIon, invalidSyntax)
errorHandler(notification, logEnvironment, "error", verbose=verbose)
} else if (stringr::str_detect(neutralLoss, moleculeRegex) == FALSE) {
notification <- paste0(locationSpecifierNeutral, neutralLoss, invalidSyntax)
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
} else if (is.na(productIon) == FALSE) {
if (stringr::str_detect(productIon, moleculeRegex) == FALSE) {
notification <- paste0(locationSpecifierProduct, productIon, invalidSyntax)
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
} else {
notification <- paste0(locationSpecifierProduct, "for ", colnamesMoleculeFileExp[2], " must be provided.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
duplicate <- anyDuplicated(data[[1]])
if (duplicate != 0) {
notification <- paste0("In molecule file: Molecule ", data[[1]][duplicate], " present in duplicate.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
if(verbose){message(date(), " :: checking molecule data structure [OK]\n")}
return(data.frame(data))
}
# Check if molecule data makes sense
checkMoleculeDataLogic <- function(extractedData, UltraHighRes, CorrectTracerImpurity, ElementList, logEnvironment, verbose) {
if(verbose){message(date(), " :: :: checking molecule data logic ...")}
molecules <- names(extractedData)
numberFragments <- list()
tracers <- list()
for (molecule in molecules) {
numberFragments[[molecule]] <- sum(stringr::str_detect(names(extractedData[[molecule]]), "Fragment"))
tracers[[molecule]] <- c()
tracers[[molecule]][1] <- length(extractedData[[molecule]]$Fragment_1$Tracer)
if (numberFragments[[molecule]] > 1) {
tracers[[molecule]][2] <- length(extractedData[[molecule]]$Fragment_2$Tracer)
} else {
tracers[[molecule]][2] <- 0
}
if (sum(tracers[[molecule]]) == 0) {
notification <- paste0("In molecule file: No tracer element provided for molecule ", molecule, ".")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
if (UltraHighRes == TRUE) {
for (molecule in molecules) {
if (numberFragments[[molecule]] != 1) {
notification <- paste0("In molecule file: More than one fragment provided for molecule ", molecule, ", but ultra high resolution correction is not compatible with MS/MS data.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
} else {
for (molecule in molecules) {
if ((tracers[[molecule]][1] > 1) || (tracers[[molecule]][2] > 1)) {
notification <- paste0("In molecule file: More than one tracer element provided for ms ion/product Ion and/or neutral loss of molecule ", molecule, ", but normal resolution correction is only compatible with a single tracer element.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
if ((tracers[[molecule]][1] > 0) && (tracers[[molecule]][2] > 0)) {
if (extractedData[[molecule]]$Fragment_1$IDTracer != extractedData[[molecule]]$Fragment_2$IDTracer) {
notification <- paste0("In molecule file: Tracer elements in product ion and neutral loss of molecule ", molecule, " do not match.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
}
# Check for duplicate elements in the molecule formula
for (molecule in molecules) {
duplicatesPresent <- 0
for (fragmentNo in seq_len(numberFragments[[molecule]])) {
fragment <- paste0("Fragment_", fragmentNo)
duplicatesPresent <- duplicatesPresent + anyDuplicated(names(extractedData[[molecule]][[fragment]]$Element)) + anyDuplicated(names(extractedData[[molecule]][[fragment]]$Tracer))
}
if (duplicatesPresent) {
notification <- paste0("In molecule file: Molecule ", molecule, " contains duplicate elements.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
elementsProvided <- names(ElementList)
for (molecule in molecules) {
for (fragmentNo in seq_len(numberFragments[[molecule]])) {
fragment <- paste0("Fragment_", fragmentNo)
elementsFragment <- extractedData[[molecule]][[fragment]]$Element
if (fragmentNo == 1) {
fragmentString = "ms ion/product ion"
} else {
fragmentString = "neutral loss"
}
commonString <- paste0("In molecule file: In ", fragmentString, " of molecule ", molecule, ": ")
# Check if elements in the molecule formula are present in the element file
if (anyNA(match(names(elementsFragment), elementsProvided))) {
notification <- paste0(commonString, "One or more elements in the provided formula were not found in the element file.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Do this only if the fragment contains a tracer
if (tracers[[molecule]][[fragmentNo]] > 0) {
tracersFragment <- extractedData[[molecule]][[fragment]]$Tracer
# Check if tracer elements in the molecule formula are also present as non-tracer elements (which gives the total number of atoms, not just the tracer
# atoms)
if (anyNA(match(names(tracersFragment), names(elementsFragment)))) {
notification <- paste0(commonString, "Information on total atom count (labelled + unlabelled) missing for tracer element(s).")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# For each tracer element found in the molecule formula, check the number of tracer atoms exceeds the total number of atoms of that element
for (tracer in names(tracersFragment)) {
if (tracersFragment[[tracer]] > elementsFragment[[tracer]]) {
notification <- paste0(commonString, "Number of tracer isotopes of element ", tracer, " exceeds number of atoms of that element present in total.")
errorHandler(notification, logEnvironment, "error")
}
# For each tracer element, check if a mass shift is provided in the element file
TracerMassShift <- ElementList[[tracer]]$Tracer.isotope.mass.shift
if (TracerMassShift == 0) {
notification <- paste0(commonString, "No mass shift information for tracer element ", tracer, " provided in element file.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Given correction for tracer impurity is active, for each tracer element, check if purity is provided in the element file
if (CorrectTracerImpurity == TRUE) {
for (tracer in names(tracersFragment)) {
if (ElementList[[tracer]]$Tracer.purity == 0) {
notification <- paste0(commonString, "No tracer purity information for tracer element ", tracer, " provided in element file, but correction for tracer impurity is active.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
}
}
}
if(verbose){message(date(), " :: :: checking molecule data logic [OK]")}
}
checkElementDataStructure <- function(data, logEnvironment, verbose) {
if(verbose){message(date(), " :: checking element data structure ...")}
# Check number of columns
if (ncol(data) != 4) {
notification <- paste0(ncol(data), " columns detected in Element File but 4 are required.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Check column names
colnamesElementFileExp <- c("element", "isotope abundance_mass shift", "tracer isotope mass shift", "tracer purity")
colnamesElementFile <- tolower(colnames(data))
for (col in seq_len(ncol(data))) {
if (colnamesElementFileExp[col] != colnamesElementFile[col]) {
notification <- paste0("Column names '", paste0(colnamesElementFile, collapse = ", "), "' found in the element file do not match those expected for the file: '",
paste0(colnamesElementFileExp, collapse = ", "), "'.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# Check if there are rows
if (nrow(data) == 0) {
notification <- "No rows found in element file."
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
# Use regular expressions to check column data
regexVector <- c()
regexVector[1] <- "^[A-Z][a-z]?$"
regexVector[2] <- "(((^1|^1\\.[0]+|^[0]\\.[0-9]+)_(|-)[0-9])(/((1|1\\.[0]+|[0]\\.[0-9]+)_(|-)[0-9]))*)$"
regexVector[3] <- "^(|-)[1-9]$"
regexVector[4] <- "^1$|^1\\.[0]+$|^[0]\\.[0-9]+$"
notificationVector <- c()
notificationVector[1] <- " is no valid element symbol."
notificationVector[2] <- " doesn't show appropriate isotope abundance/mass shift definition syntax."
notificationVector[3] <- " is no valid tracer isotope mass shift definition."
notificationVector[4] <- " is no valid tracer purity definition."
for (col in seq_len(ncol(data))) {
currentCol <- data[[col]]
# This conversion of NA to empty string for columns 1 and 2 is done because NA values in columns 3 and 4 must not throw an error
for (row in seq_len(nrow(data))) {
if (is.na(currentCol[row]) && col == (1 || 2)) {
currentCol[row] <- ""
}
if (is.na(currentCol[row]) == FALSE) {
if (stringr::str_detect(currentCol[row], regexVector[col]) == FALSE) {
locationSpecifier <- paste0("In element file column ", col, ", row ", row, ": ")
notification <- paste0(locationSpecifier, currentCol[row], notificationVector[col])
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
}
# Check for duplicate elements
duplicate <- anyDuplicated(data[[1]])
if (duplicate != 0) {
notification <- paste0("In element file: Element ", data[[1]][duplicate], " present in duplicate.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
if(verbose){message(date(), " :: checking element data structure [OK]\n")}
return(data.frame(data))
}
# Check if element data makes sense
checkElementDataLogic <- function(extractedData, UltraHighRes, logEnvironment, verbose) {
#if(verbose){message(date(), " [checkElementDataLogic]")}
if(verbose){message(date(), " :: :: checking element data logic ...")}
for (element in names(extractedData)) {
if (any(duplicated(as.data.frame(extractedData[[element]]$Isotopes)$MassShift))) {
notification <- paste0("In element file: Duplicated MassShift for element ", element, ".")
errorHandler(notification, logEnvironment, "error")
}
# Without rounding, Si doesn't work as the sum is 1.000001. Howver, should we really round here?
if (round(sum(data.frame(extractedData[[element]][["Isotopes"]])[, 1]), 5) > 1) {
notification <- paste0("In element file: Sum of isotope abundances of element ", element, " is > 1.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
# In case of UHR mode, check if the mass shift of the tracers is also found in the tracer elements natural isotopes. If not, probabilities cannot be
# calculated
if (UltraHighRes) {
for (element in names(extractedData)) {
TracerMassShift <- extractedData[[element]]$Tracer.isotope.mass.shift
if (TracerMassShift > 0 && is.na(match(TracerMassShift, as.data.frame(extractedData[[element]]$Isotopes)$MassShift))) {
notification <- paste0("In element file: Mass shift '", TracerMassShift, "' of tracer element ", element, " is not found in the natural isotope information of that element.")
errorHandler(notification, logEnvironment, "error", verbose=verbose)
}
}
}
if(verbose){message(date(), " :: :: checking element data logic [OK]")}
}
readFileByExt <- function(file, verbose) {
fileExt <- tools::file_ext(file)
if (fileExt == "") {
stop(date(), " :: no file extension for file: ", file, "\n")
} else {
if(verbose){message(date(), " :: :: detected file format: ", fileExt)}
if (fileExt %in% c("xls", "xlsx")) {
fileData <- readxl::read_excel(file)
} else if (fileExt == "csv") {
fileData <- readr::read_csv(file)
} else {
stop(date(), " :: unsupported file format: ", fileExt, "\n")
}
}
return(fileData)
}
convertEnrichmentList2matrix <- function(input, verbose) {
if(verbose){message(date(), " :: :: converting enrichment results into a matrix ...")}
# matrix with sampleIds as columns and mean enrichment for molecule on row
m <- matrix(ncol = length(input), nrow = length(input[[1]]))
colnames(m) <- names(input)
rownames(m) <- names(input[[1]])
# TODO: quick and dirty loop. find more elegant solution !!
for (i in seq_len(length(input))) {
for (i2 in seq_len(length(input[[i]]))) {
m[i2, i] <- as.numeric(input[[i]][[i2]])
} #i2
} #i
if(verbose){message(date(), " :: :: converting enrichment results into a matrix [OK]")}
return(m)
}
convert2matrix <- function(input) {
vec.transitions <- vector()
# we need to loop over all samples to really get all transitions
for (sample in names(input)) {
for (molecule in names(input[[sample]])) {
vec.transitions <- c(vec.transitions, names(input[[sample]][[molecule]][[1]]))
} #molecule
} #sample
transitions.unique <- unique(vec.transitions)
templateMat <- matrix(NA, ncol = length(names(input)), nrow = length(transitions.unique))
colnames(templateMat) <- names(input)
rownames(templateMat) <- transitions.unique
# now populate the four matrices
list.corrMat <- list()
for (corrMat in names(input[[1]][[1]])) {
templateMat2 <- templateMat
for (sample in names(input)) {
for (molecule in names(input[[sample]])) {
for (transition in names(input[[sample]][[molecule]][[corrMat]])) {
templateMat2[transition, sample] <- input[[sample]][[molecule]][[corrMat]][[transition]]
} #transition
} #molecule
} #sample
list.corrMat[[corrMat]] <- templateMat2
} #corrMat
return(list.corrMat)
} #convert2matrix
defineOutputFilenames <- function(logEnvironment,FileOut,FileOutFormat,
CalculateMeanEnrichment,CorrectAlsoMonoisotopic) {
#DEFINE NAMES OF OUTPUT FILES
logEnvironment$param$LogfileName <-
paste0(logEnvironment$param$NamePrefix, "_", FileOut, ".log")
CorrectedDataNamesBase <-
c("Corrected",
"CorrectedFractions",
"Residuals",
"RelativeResiduals")
if (CorrectAlsoMonoisotopic) {
CorrectedDataNamesBase <-
c(
CorrectedDataNamesBase,
"CorrectedMonoisotopic",
"CorrectedMonoisotopicFractions"
)
}
if (CalculateMeanEnrichment) {
CorrectedDataNames <-
c(CorrectedDataNamesBase, "MeanEnrichment", "RawData")
}
else {
CorrectedDataNames <- c(CorrectedDataNamesBase, "RawData")
}
if (FileOutFormat == "csv") {
CorrectedDataFileNames <-
vector(mode = "character",
length = length(CorrectedDataNames))
names(CorrectedDataFileNames) <- CorrectedDataNames
for (name in CorrectedDataNames) {
CorrectedDataFileNames[name] <-
paste0(logEnvironment$param$NamePrefix,
"_",
FileOut,
"_",
name,
".",
FileOutFormat)
}
logEnvironment$param$FileOut <-
paste0(CorrectedDataFileNames, collapse = ", ")
}
else if (FileOutFormat == "xls") {
logEnvironment$param$FileOut <-
paste0(logEnvironment$param$NamePrefix,
"_",
FileOut,
".",
FileOutFormat)
CorrectedDataFileNames <- NA
}
return(list("CorrectedDataNames" = CorrectedDataNames,
"CorrectedDataNamesBase" = CorrectedDataNamesBase,
"CorrectedDataFileNames" = CorrectedDataFileNames))
}
#WRITE CORRECTED DATA TO FILE
writeCorrectionResultsToFile <- function(CorrectedDataOutput,NamesCorrectedOutput,logEnvironment, verbose) {
if(verbose){message(date()," :: writing results to ",logEnvironment$param$FileOut," ...")}
if (logEnvironment$param$FileOutFormat == "xls") {
WriteXLS::WriteXLS(
CorrectedDataOutput,
file.path(logEnvironment$param$OutputDirectory, logEnvironment$param$FileOut),
perl = "perl",
row.names = TRUE
)
} else if (logEnvironment$param$FileOutFormat == "csv") {
for (name in NamesCorrectedOutput$CorrectedDataNames) {
utils::write.csv(
CorrectedDataOutput[[name]],
file = file.path(
logEnvironment$param$OutputDirectory,
NamesCorrectedOutput$CorrectedDataFileNames[name]
)
)
}
}
if(verbose){message(date()," :: writing results to ",logEnvironment$param$FileOut," [OK]\n")}
}
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