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# Computation of isotope combinations, associated probabilities and mass shifts
# for an element
#' @importFrom stringr str_c
IsoCombinationsMaster <- function(MoleculeData, MoleculeName, MoleculeNo, Fragment, ElementInfo, CalculationThreshold, CorrectTracerImpurity, CorrectTracerElementCore) {
MoleculeFragmentData <- MoleculeData[[stringr::str_c("Fragment_", Fragment)]] # get individual fragment data
Transitions <- MoleculeData[["Transitions"]]
NumberTransitions <- nrow(Transitions)
NumberTracers <- length(MoleculeFragmentData[["Tracer"]])
# Isotope combinations for tracer element
IsoCombinationsTracerResult <- IsoCombinationsTracer(MoleculeFragmentData=MoleculeFragmentData,
Fragment=Fragment,
ElementInfo = ElementInfo,
Transitions=Transitions,
NumberTracers=NumberTracers,
CorrectTracerImpurity=CorrectTracerImpurity,
CorrectTracerElementCore=CorrectTracerElementCore,
CalculationThreshold=CalculationThreshold)
ProbTracerList <- IsoCombinationsTracerResult$ProbTracerList
MassShiftTracerList <- IsoCombinationsTracerResult$MassShiftTracerList
NumberIsoCombTracerEff <- IsoCombinationsTracerResult$NumberIsoCombTracerEff
IsotopesTracer <- IsoCombinationsTracerResult$IsotopesTracer
LabelPresent <- IsoCombinationsTracerResult$LabelPresent
# Isotope combinations for non-tracer elements
if (NumberTracers > 0) {
IDTracer <- MoleculeFragmentData[["IDTracer"]]
} else {
IDTracer <- NA
}
IsoCombinationsNonTracerResult <- IsoCombinationsNonTracer(MoleculeFragmentData=MoleculeFragmentData,
Fragment=Fragment,
ElementInfo=ElementInfo,
NumberTracers=NumberTracers,
IDTracer=IDTracer,
CalculationThreshold=CalculationThreshold)
ProbElemList <- IsoCombinationsNonTracerResult$ProbElemList
MassShiftElemList <- IsoCombinationsNonTracerResult$MassShiftElemList
NumberIsoCombEff <- IsoCombinationsNonTracerResult$NumberIsoCombEff
IsotopesElem <- IsoCombinationsNonTracerResult$IsotopesElem
# Compute tracer impurity combinations
ProbTracerImpurityList <- list()
MassShiftTracerImpurityList <- list()
NumberImpurityCombEff <- list()
if (CorrectTracerImpurity) {
if (NumberTracers > 0) {
IsoCombinationsImpurityResult <- IsoCombinationsTracerImpurity(MoleculeFragmentData=MoleculeFragmentData,
ElementInfo=ElementInfo,
Transitions=Transitions,
NumberTransitions=NumberTransitions,
IDTracer=IDTracer,
LabelPresent=LabelPresent,
CalculationThreshold=CalculationThreshold)
ProbTracerImpurityList <- IsoCombinationsImpurityResult$ProbTracerImpurityList
MassShiftTracerImpurityList <- IsoCombinationsImpurityResult$MassShiftTracerImpurityList
NumberImpurityCombEff <- IsoCombinationsImpurityResult$NumberImpurityCombEff
}
} else {
ProbTracerImpurityList <- "No Correction for Tracer Impurity performed"
MassShiftTracerImpurityList <- "No Correction for Tracer Impurity performed"
NumberImpurityCombEff <- "No Correction for Tracer Impurity performed"
} #CorrectTracerImpurity=TRUE
IsoCombinationsResult <- list(ProbTracerList = ProbTracerList, ProbElemList = ProbElemList, ProbTracerImpurityList = ProbTracerImpurityList, MassShiftTracerList = MassShiftTracerList,
MassShiftElemList = MassShiftElemList, MassShiftTracerImpurityList = MassShiftTracerImpurityList, NumberIsoCombEff = unlist(NumberIsoCombEff),
NumberImpurityCombEff = NumberImpurityCombEff, NumberIsoCombTracerEff = unlist(NumberIsoCombTracerEff), IsotopesTracer = IsotopesTracer, IsotopesElem = IsotopesElem,
LabelPresent = LabelPresent)
return(IsoCombinationsResult)
} #IsoCombinationsMaster()
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