| Type: | Package |
| Title: | United Formula Annotation (UFA) for HRMS Data Processing |
| Version: | 2.0 |
| Depends: | R (≥ 4.0) |
| Imports: | IDSL.IPA (≥ 2.7), readxl |
| Suggests: | GA |
| Author: | Sadjad Fakouri-Baygi
 [aut],
Dinesh Barupal
[cre, aut] |
| Maintainer: | Dinesh Barupal <dinesh.barupal@mssm.edu> |
| Description: | A pipeline to annotate chromatography peaks from the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120> with molecular formulas of a prioritized chemical space using an isotopic profile matching approach. The 'IDSL.UFA' workflow only requires mass spectrometry level 1 (MS1) data for formula annotation. The 'IDSL.UFA' methods was described in <doi:10.1021/acs.analchem.2c00563> . |
| License: | MIT + file LICENSE |
| URL: | https://github.com/idslme/idsl.ufa |
| BugReports: | https://github.com/idslme/idsl.ufa/issues |
| Encoding: | UTF-8 |
| Archs: | i386, x64 |
| NeedsCompilation: | no |
| Packaged: | 2023-05-18 19:31:04 UTC; sfbaygi |
| Repository: | CRAN |
| Date/Publication: | 2023-05-18 21:20:02 UTC |
UFA IPDB Merger
Description
To merge multiple IPDBs into one IPDB
Usage
UFA_IPdbMerger(path, vecIPDB)
Arguments
path |
path |
vecIPDB |
a vector of IPDBs |
Value
IPDB
UFA PubChem Formula Extraction
Description
This module is to extract molecular formulas from a database.
Usage
UFA_PubChem_formula_extraction(path)
Arguments
path |
path to store information |
Value
Molecular formulas in https://pubchem.ncbi.nlm.nih.gov/ are stored in the provided 'path' in the .txt format.
References
Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, Zaslavsky L, Zhang J, Bolton EE. PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res., 2021 Jan 8; 49(D1):D1388–D1395 , doi:10.1093/nar/gkaa971.
IPDBs from UFA Enumerated Chemical Space (ECS) approach
Description
This function produces the isotopic profile database using the UFA enumerated chemical space (ECS) approach.
Usage
UFA_enumerated_chemical_space(PARAM_ECS)
Arguments
PARAM_ECS |
A dataframe of the molecular formula constraints in the UFA spreadsheet |
IPDBs from UFA Enumerated Chemical Space (ECS) xlsx Analyzer
Description
This function evaluates the molecular formula generation constraints in the spreadsheet to create the isotopic profile database.
Usage
UFA_enumerated_chemical_space_xlsxAnalyzer(spreadsheet)
Arguments
spreadsheet |
UFA spreadsheet |
IPDB from a Molecular Formulas Source
Description
This function produces IPDB from a molecular formula source (a .csv/.txt/.xlsx file).
Usage
UFA_formula_source(PARAM_FormSource)
Arguments
PARAM_FormSource |
PARAM_FormSource is an internal variable of the IDSL.UFA package. |
Value
an IPDB is saved in the destination address
UFA Formula Source xlsxAnalyzer
Description
This function evaluates the parameter spreadsheet for score coefficients optimization.
Usage
UFA_formula_source_xlsxAnalyzer(spreadsheet)
Arguments
spreadsheet |
The parameter spreadsheet in the .xlsx format. |
Value
a processed parameter to feed the 'UFA_molecular_formulas_source' function.
UFA Locate regex
Description
Locate indices of the pattern in the string
Usage
UFA_locate_regex(string, pattern, ignore.case = FALSE, perl = FALSE, fixed = FALSE,
useBytes = FALSE)
Arguments
string |
a string as character |
pattern |
a pattern to screen |
ignore.case |
ignore.case |
perl |
perl |
fixed |
fixed |
useBytes |
useBytes |
Details
This function returns 'NULL' when no matches are detected for the pattern.
Value
A 2-column matrix of location indices. The first and second columns represent start and end positions, respectively.
Examples
pattern <- "Cl"
string <- "NaCl.5HCl"
Location_Cl <- UFA_locate_regex(string, pattern)
Score Coefficients Corrector for MolecularFormulaAnnotationTable
Description
This function updates ranking orders of the individual MolecularFormulaAnnotationTable when score coefficients changed.
Usage
UFA_score_coefficients_corrector(input_annotated_molf_address,
output_annotated_molf_address, scoreCoefficients, number_processing_threads = 1)
Arguments
input_annotated_molf_address |
Address to load the individual MolecularFormulaAnnotationTables. |
output_annotated_molf_address |
Address to save the individual MolecularFormulaAnnotationTables. |
scoreCoefficients |
A vector of five numbers representing coefficients of the identification score function. |
number_processing_threads |
Number of processing threads for multi-threaded computations. |
UFA Score Coefficient Workflow
Description
This function runs the score optimization workflow.
Usage
UFA_score_function_optimization(PARAM_ScoreFunc)
Arguments
PARAM_ScoreFunc |
PARAM_ScoreFunc from the 'UFA_score_function_optimization_xlsxAnalyzer' module |
UFA Score Optimization xlsx Analyzer
Description
This function evaluates the parameter spreadsheet for score coefficients optimization.
Usage
UFA_score_function_optimization_xlsxAnalyzer(spreadsheet)
Arguments
spreadsheet |
The parameter spreadsheet in the .xlsx format. |
Value
a processed parameter to feed the 'UFA_score_function_optimization' function.
UFA Workflow
Description
This function executes the UFA workflow in order.
Usage
UFA_workflow(spreadsheet)
Arguments
spreadsheet |
UFA spreadsheet |
Value
This function organizes the UFA file processing for better performance using the template spreadsheet.
UFA xlsx Analyzer
Description
This function processes the spreadsheet of the UFA parameters to ensure the parameter inputs are consistent with the requirements of the IDSL.UFA pipeline.
Usage
UFA_xlsxAnalyzer(spreadsheet)
Arguments
spreadsheet |
UFA spreadsheet |
Value
This function returns the UFA parameters to feed the UFA_workflow function.
aggregatedIPdbListGenerator
Description
aggregatedIPdbListGenerator
Usage
aggregatedIPdbListGenerator(MassMAIso)
Arguments
MassMAIso |
MassMAIso |
Value
AggregatedList
Aligned Molecular Formula Annotator
Description
This function detects frequent molecular formulas across multiple samples on the aligned peak table matrix.
Usage
aligned_molecular_formula_annotator(PARAM)
Arguments
PARAM |
a parameter driven from the UFA_xlsxAnalyzer module. |
Organic Class Detection by Repeated Unit Patterns
Description
This function sorts a vector of molecular formulas to aggregate organic compound classes with repeated/non-repeated substructure units. This function only works for molecular formulas with following elements: c("As", "Br", "Cl", "Na", "Se", "Si", "B", "C", "F", "H", "I", "K", "N", "O", "P", "S")
Usage
detect_formula_sets(molecular_formulas, ratio_delta_HBrClFI_C = 2,
mixed.HBrClFI.allowed = FALSE, min_molecular_formula_class = 2,
max_number_formula_class = 100, number_processing_threads = 1)
Arguments
molecular_formulas |
a vector of molecular formulas |
ratio_delta_HBrClFI_C |
c(2, 1/2, 0). 2 to detect structures with linear carbon chains such as PFAS, lipids, chlorinated paraffins, etc. 1/2 to detect structures with cyclic chains such as PAHs. 0 to detect molecular formulas with a fixed structures but changing H/Br/Cl/F/I atoms similar to PCBs, PBDEs, etc. |
mixed.HBrClFI.allowed |
mixed.HBrClFI.allowed = c(TRUE, FALSE). Select 'FALSE' to detect halogenated-saturated compounds similar to PFOS or select 'TRUE' to detect mixed halogenated compounds with hydrogen. |
min_molecular_formula_class |
minimum number of molecular formulas in each class. This number should be greater than or equal to 2. |
max_number_formula_class |
maximum number of molecular formulas in each class |
number_processing_threads |
Number of processing threads for multi-threaded computations. |
Value
A matrix of clustered classes of organic molecular formulas.
Examples
molecular_formulas <- c("C3F7O3S", "C4F9O3S", "C5F11O3S", "C6F9O3S", "C8F17O3S",
"C9F19O3S", "C10F21O3S", "C7ClF14O4", "C10ClF20O4", "C11ClF22O4", "C11Cl2F21O4",
"C12ClF24O4")
##
ratio_delta_HBrClFI_C <- 2 # to aggregate polymeric classes
mixed.HBrClFI.allowed <- FALSE # To detect only halogen saturated classes
min_molecular_formula_class <- 2
max_number_formula_class <- 20
##
classes <- detect_formula_sets(molecular_formulas, ratio_delta_HBrClFI_C,
mixed.HBrClFI.allowed, min_molecular_formula_class, max_number_formula_class,
number_processing_threads = 1)
Element Sorter
Description
This module sorts 84 non-labeled and 14 labeled elements in the periodic table for molecular formula deconvolution and isotopic profile calculation.
Usage
element_sorter(ElementList = "all", alphabeticalOrder = TRUE)
Arguments
ElementList |
A string vector of elements needed for isotopic profile calculation. The default value for this parameter is a vector string of entire elements. |
alphabeticalOrder |
'TRUE' should be used to sort the elements for elemental deconvolution (default value), 'FALSE' should be used to keep the input order. |
Value
Elements |
A string vector of elements (alphabetically sorted or unsorted) |
massAbundanceList |
A list of isotopic mass and abundance of elements. |
Valence |
A vector of electron valences. |
Examples
EL_mass_abundance_val <- element_sorter()
extended SENIOR rule check
Description
This function checks whether a molecular formula follows the extended SENIOR rule.
Usage
extendedSENIORrule(mol_vec, valence_vec, ionization_correction = 0)
Arguments
mol_vec |
A vector of the deconvoluted molecular formula |
valence_vec |
A vector of the valences from the molecular formula. Valences may be acquired from the 'IUPAC_Isotopes' data. |
ionization_correction |
A number to compensate for the ionization losses/gains. For example, ‘-1' for [M+H/K/Na] ionization pathways and '+1’ for [M-H] ionization pathway. |
Value
rule2 |
TURE for when the molecular formula passes the rule and FALSE for when the molecular formula fails to pass the rule. |
Formula Adduct Calculator
Description
This function takes a formula and a vector of ionization pathways and returns the adduct formulas.
Usage
formula_adduct_calculator(molecular_formula, IonPathways)
Arguments
molecular_formula |
molecular formula |
IonPathways |
A vector of ionization pathways. Pathways should be like [Coeff*M+ADD1-DED1+...] where "Coeff" should be an integer between 1-9 and ADD1 and DED1 may be ionization pathways. ex: 'IonPathways <- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")' |
Value
A vector of adduct formulas
Examples
molecular_formula = "C15H10O7"
IonPathways = c("[M+]","[M+H]","[M+H20+H]","[M+Na]")
Formula_adducts <- formula_adduct_calculator(molecular_formula, IonPathways)
Molecular Formula Vector Generator
Description
This function convert a molecular formulas into a numerical vector
Usage
formula_vector_generator(molecular_formula, Elements, LElements = length(Elements),
allowedRedundantElements = FALSE)
Arguments
molecular_formula |
molecular formula |
Elements |
a string vector of elements. This value must be driven from the 'element_sorter' function. |
LElements |
number of elements. To speed up loop calculations, consider calculating the number of elements outside of the loop. |
allowedRedundantElements |
'TRUE' should be used to deconvolute molecular formulas with redundant elements (e.g. CO2CH3O), and 'FALSE' should be used to skip such complex molecular formulas.(default value) |
Value
a numerical vector for the molecular formula. This function returns a vector of -Inf values when the molecular formula has elements not listed in the 'Elements' string vector.
Examples
molecular_formula <- "[13]C2C12H2Br5Cl3O"
Elements_molecular_formula <- c("[13]C", "C", "H", "O", "Br", "Cl")
EL <- element_sorter(ElementList = Elements_molecular_formula, alphabeticalOrder = TRUE)
Elements <- EL[["Elements"]]
LElements <- length(Elements)
##
mol_vec <- formula_vector_generator(molecular_formula, Elements, LElements,
allowedRedundantElements = TRUE)
##
regenerated_molecular_formula <- hill_molecular_formula_printer(Elements, mol_vec)
Print Hill Molecular Formula
Description
This function produces molecular formulas from a list numerical vectors in the Hill notation system
Usage
hill_molecular_formula_printer(Elements, MolVecMat, number_processing_threads = 1)
Arguments
Elements |
A vector string of the used elements. |
MolVecMat |
A matrix of numerical vectors of molecular formulas in each row. |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Value
A vector of molecular formulas
Examples
Elements <- c("C", "H", "O", "N", "Br", "Cl")
MoleFormVec1 <- c(2, 6, 1, 0, 0, 0) # C2H6O
MoleFormVec2 <- c(8, 10, 2, 4, 0 ,0) # C8H10N4O2
MoleFormVec3 <- c(12, 2, 1, 0, 5, 3) # C12H2Br5Cl3O
MolVecMat <- rbind(MoleFormVec1, MoleFormVec2, MoleFormVec3)
H_MolF <- hill_molecular_formula_printer(Elements, MolVecMat)
Multiplicative Identification Score for the IDSL.UFA pipeline
Description
This function calculates the score values to rank candidate molecular formulas for a mass spectrometry-chromatography peak.
Usage
identificationScoreCalculator(scoreCoefficients, nIisotopologues, PCS, RCS, NEME,
R13C_PL, R13C_IP)
Arguments
scoreCoefficients |
A vector of seven numbers equal or greater than 0 |
nIisotopologues |
Number of isotopologues in the theoretical isotopic profiles. |
PCS |
PCS (per mille) |
RCS |
RCS (percentage) |
NEME |
NEME (mDa) |
R13C_PL |
R13C of the peak from IDSL.IPA peaklists |
R13C_IP |
R13C from theoretical isotopic profiles |
Ionization Pathway Deconvoluter
Description
This function deconvolutes ionization pathways into a coefficient and a numerical vector to simplify prediction ionization pathways.
Usage
ionization_pathway_deconvoluter(IonPathways, Elements)
Arguments
IonPathways |
A vector of ionization pathways. Pathways should be like [Coeff*M+ADD1-DED1+...] where "Coeff" should be an integer between 1-9 and ADD1 and DED1 may be ionization pathways. ex: 'IonPathways <- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")' |
Elements |
A vector string of the used elements |
Value
A list of adduct calculation values for each ionization pathway.
Examples
Elements <- element_sorter(alphabeticalOrder = TRUE)[["Elements"]]
IonPathways <- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")
Ion_DC <- ionization_pathway_deconvoluter(IonPathways, Elements)
Isotopic Profile Calculator
Description
This function was designed to calculate isotopic profile distributions for small molecules with masses <= 1200 Da. Nonetheless, this function may suit more complicated tasks with complex biological compounds. Details of the equations used in this function are available in the reference[1]. In this function, neighboring isotopologues are merged using the satellite clustering merging (SCM) method described in the reference[2].
Usage
isotopic_profile_calculator(MoleFormVec, massAbundanceList, peak_spacing,
intensity_cutoff, UFA_IP_memeory_variables = c(1e30, 1e-12, 100))
Arguments
MoleFormVec |
A numerical vector of the molecular formula |
massAbundanceList |
A list of isotopic mass and abundance of elements obtained from the 'element_sorter' function |
peak_spacing |
A maximum space between two isotopologues in Da |
intensity_cutoff |
A minimum intensity threshold for isotopic profiles in percentage |
UFA_IP_memeory_variables |
A vector of three variables. Default values are c(1e30, 1e-12, 100) to manage memory usage. UFA_IP_memeory_variables[1] is used to control the overall size of isotopic combinations. UFA_IP_memeory_variables[2] indicates the minimum relative abundance (RA calculated by eq(1) in the reference [1]) of an isotopologue to include in the isotopic profile calculations. UFA_IP_memeory_variables[3] is the maximum elapsed time to calculate the isotopic profile on the 'setTimeLimit' function of base R. |
Value
A matrix of isotopic profile. The first and second column represents the mass and intensity profiles, respectively.
References
[1] Fakouri Baygi, S., Crimmins, B.S., Hopke, P.K. Holsen, T.M. (2016). Comprehensive emerging chemical discovery: novel polyfluorinated compounds in Lake Michigan trout. Environmental Science and Technology, 50(17), 9460-9468, doi:10.1021/acs.est.6b01349.
[2] Fakouri Baygi, S., Fernando, S., Hopke, P.K., Holsen, T.M. and Crimmins, B.S. (2019). Automated Isotopic Profile Deconvolution for High Resolution Mass Spectrometric Data (APGC-QToF) from Biological Matrices. Analytical chemistry, 91(24), 15509-15517, doi:10.1021/acs.analchem.9b03335.
See Also
Examples
EL <- element_sorter(alphabeticalOrder = TRUE)
Elements <- EL[["Elements"]]
massAbundanceList <- EL[["massAbundanceList"]]
peak_spacing <- 0.005 # mDa
intensity_cutoff <- 1 # (in percentage)
MoleFormVec <- formula_vector_generator("C8H10N4O2", Elements)
IP <- isotopic_profile_calculator(MoleFormVec, massAbundanceList, peak_spacing,
intensity_cutoff)
Molecular Formula to IPDB
Description
A function to calculate IPDBs from a vector of molecular formulas
Usage
molecularFormula2IPdb(molecularFormulaDatabase, retentionTime = NULL, peak_spacing = 0,
intensity_cutoff_str = 1, IonPathways = "[M]+", number_processing_threads = 1,
UFA_IP_memeory_variables = c(1e30, 1e-12, 100), allowedMustRunCalculation = FALSE,
allowedVerbose = TRUE)
Arguments
molecularFormulaDatabase |
A vector string of molecular formulas OR a list of elements and molecular formula matrix |
retentionTime |
retention time |
peak_spacing |
A maximum space between isotopologues in Da to merge neighboring isotopologues. |
intensity_cutoff_str |
A minimum intensity threshold for isotopic profiles in percentage. This parameter may be a string piece of R commands using c, b, br, cl, k, s, se, and si variables corresponding to the same elements. |
IonPathways |
A vector of ionization pathways. Pathways should be like [Coeff*M+ADD1-DED1+...] where "Coeff" should be an integer between 1-9 and ADD1 and DED1 may be ionization pathways. ex: 'IonPathways <- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")' |
number_processing_threads |
number of processing cores for multi-threaded computations. |
UFA_IP_memeory_variables |
A vector of three variables. Default values are c(1e30, 1e-12, 100) to manage memory usage. UFA_IP_memeory_variables[1] is used to control the overall size of isotopic combinations. UFA_IP_memeory_variables[2] indicates the minimum relative abundance (RA calculated by eq(1) in the reference [1]) of an isotopologue to include in the isotopic profile calculations. UFA_IP_memeory_variables[3] is the maximum elapsed time to calculate the isotopic profile on the 'setTimeLimit' function of the base R. |
allowedMustRunCalculation |
c(TRUE, FALSE). A 'TRUE' allowedMustRunCalculation applies a brute-force method to calculate complex isotopic profiles. When 'TRUE', this option may significantly reduce the speed for multithreaded processing. |
allowedVerbose |
c(TRUE, FALSE). A 'TRUE' allowedVerbose provides messages about the flow of the function. |
Value
An IPDB list of isotopic profiles
References
[1] Fakouri Baygi, S., Crimmins, B.S., Hopke, P.K. Holsen, T.M. (2016). Comprehensive emerging chemical discovery: novel polyfluorinated compounds in Lake Michigan trout. Environmental Science and Technology, 50(17), 9460-9468, doi:10.1021/acs.est.6b01349.
See Also
Examples
library(IDSL.UFA, attach.required = TRUE)
molecular_formula <- c("C13F8N8O2", "C20H22", "C8HF16ClSO3", "C12Cl10", "C123H193N35O37")
peak_spacing <- 0.005 # in Da for QToF instruments
# Use this piece of code for intensity cutoff to preserve significant isotopologues
intensity_cutoff_str <- "if (s>0 & si>0) {min(c(c, 10, si*3, s*4))}
else if (s>0 & si==0) {min(c(c, 10, s*4))}
else if (s==0 & si>0) {min(c(c, 10, si*3))}
else if (s==0 & si==0) {min(c(c, 10))}"
UFA_IP_memeory_variables <- c(1e30, 1e-12, 100)
IonPathways <- c("[M+H]+", "[M+Na]+", "[M-H2O+H]+")
number_processing_threads <- 2
listIsoProDataBase <- molecularFormula2IPdb(molecular_formula, retentionTime = NULL,
peak_spacing, intensity_cutoff_str, IonPathways, number_processing_threads,
UFA_IP_memeory_variables, allowedMustRunCalculation = FALSE, allowedVerbose = TRUE)
save(listIsoProDataBase, file = "listIsoProDataBase.Rdata")
Molecular Formula Annotator
Description
This module annotates candidate molecular formulas in the peaklists from the IDSL.IPA pipeline using isotopic profiles.
Usage
molecular_formula_annotator(IPDB, spectraList, peaklist, selectedIPApeaks,
massAccuracy, maxNEME, minPCS, minNDCS, minRCS, scoreCoefficients, RTtolerance = NA,
correctedRTpeaklist = NULL, exportSpectraParameters = NULL, number_processing_threads = 1)
Arguments
IPDB |
An isotopic profile database produced by the IDSL.UFA functions. |
spectraList |
a list of mass spectra in each chromatogram scan. |
peaklist |
Peaklist from the IDSL.IPA pipeline |
selectedIPApeaks |
selected IPA peaklist |
massAccuracy |
Mass accuracy in Da |
maxNEME |
Maximum value for Normalized Euclidean Mass Error (NEME) in mDa |
minPCS |
Minimum value for Profile Cosine Similarity (PCS) |
minNDCS |
Minimum value for Number of Detected Chromatogram Scans (NDCS) |
minRCS |
Minimum value for Ratio of Chromatogram Scans (RCS) in percentage |
scoreCoefficients |
A vector of five numbers representing coefficients of the identification score |
RTtolerance |
Retention time tolerance (min) |
correctedRTpeaklist |
corrected retention time peaklist |
exportSpectraParameters |
Parameters for export MS/MS match figures |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Value
A dataframe of candidate molecular formulas
molecular_formula_elements_filter
Description
molecular_formula_elements_filter
Usage
molecular_formula_elements_filter(molecularFormulaMatrix, Elements)
Arguments
molecularFormulaMatrix |
molecularFormulaMatrix |
Elements |
Elements |
Value
a list of molecularFormulaMatrix and elementSorterList.
Molecular Formula Database Producer
Description
This function generates an efficient database for molecular formula matching against a database.
Usage
molecular_formula_library_generator(entire_molecular_formulas)
Arguments
entire_molecular_formulas |
A string vector of molecular formulas (redundancy is allowed) |
Value
A vector of frequency of molecular formulas in the database.
Examples
entire_molecular_formulas <- c("C2H6O", "C2H6O", "C2H6O", "C2H6O", "CH4O", "CH4O",
"CH4O", "NH4", "C6H12O6")
db <- molecular_formula_library_generator(entire_molecular_formulas)
freq <- db[c("C6H12O6", "CH4O")]
Molecular Formula Library Search
Description
This function attempts to match candidate molecular formulas against a library of molecular formulas using a set of ionization pathways.
Usage
molecular_formula_library_search(MolecularFormulaAnnotationTable, MFlibrary,
IonPathways, number_processing_threads = 1)
Arguments
MolecularFormulaAnnotationTable |
A molecular formula annotation table from the 'molecular_formula_annotator' module. |
MFlibrary |
A library of molecular formulas generated using the 'molecular_formula_library_generator' module. |
IonPathways |
A vector of ionization pathways. Pathways should be like [Coeff*M+ADD1-DED1+...] where "Coeff" should be an integer between 1-9 and ADD1 and DED1 may be ionization pathways. ex: 'IonPathways <- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")' |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Monoisotopic Mass Calculator
Description
This function calculates monoisotopic mass of a molecular formula
Usage
monoisotopicMassCalculator(MoleFormVec, massAbundanceList,
LElements = length(massAbundanceList))
Arguments
MoleFormVec |
A numerical vector molecular formula |
massAbundanceList |
A list of isotopic mass and abundance of elements obtained from the 'element_sorter' function |
LElements |
length of elements |
Value
The monoisotopic mass
Examples
Elements <- c("C", "H", "O")
MoleFormVec <- c(2, 6, 1) # C2H6O
EL_mass_abundance <- element_sorter(ElementList = Elements, alphabeticalOrder = FALSE)
massAbundanceList <- EL_mass_abundance[["massAbundanceList"]]
MImass <- monoisotopicMassCalculator(MoleFormVec, massAbundanceList)
Score Coefficient Evaluation
Description
This function evaluates the efficiency of the optimization process.
Usage
scoreCoefficientsEvaluation(PARAM_ScoreFunc)
Arguments
PARAM_ScoreFunc |
PARAM_ScoreFunc is a variable derived from the 'UFA_coefficient_xlsxAnalyzer' function |
Coefficients Score Optimization
Description
This function optimizes the coefficients of the score function.
Usage
scoreCoefficientsOptimization(PARAM_ScoreFunc)
Arguments
PARAM_ScoreFunc |
PARAM_ScoreFunc is a variable derived from the 'UFA_score_function_optimization_xlsxAnalyzer' function |
Zero Score Function
Description
This function generates the input for the score optimization.
Usage
scoreCoefficientsReplicate(PARAM_ScoreFunc)
Arguments
PARAM_ScoreFunc |
PARAM_ScoreFunc is a variable derived from the 'UFA_coefficient_xlsxAnalyzer' function |