Learn R Programming

IDSL.UFA (version 2.0)

United Formula Annotation (UFA) for HRMS Data Processing

Description

A pipeline to annotate chromatography peaks from the 'IDSL.IPA' workflow 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 .

Copy Link

Version

Install

install.packages('IDSL.UFA')

Monthly Downloads

210

Version

2.0

License

MIT + file LICENSE

Issues

0

Pull Requests

0

Stars

8

Forks

1

Maintainer

Dinesh Barupal

Last Published

May 18th, 2023

Functions in IDSL.UFA (2.0)

hill_molecular_formula_printer

Print Hill Molecular Formula
UFA_xlsxAnalyzer

UFA xlsx Analyzer
element_sorter

Element Sorter
formula_adduct_calculator

Formula Adduct Calculator
UFA_workflow

UFA Workflow
formula_vector_generator

Molecular Formula Vector Generator
extendedSENIORrule

extended SENIOR rule check
detect_formula_sets

Organic Class Detection by Repeated Unit Patterns
monoisotopicMassCalculator

Monoisotopic Mass Calculator
aggregatedIPdbListGenerator

aggregatedIPdbListGenerator
molecularFormula2IPdb

Molecular Formula to IPDB
UFA_score_coefficients_corrector

Score Coefficients Corrector for MolecularFormulaAnnotationTable
aligned_molecular_formula_annotator

Aligned Molecular Formula Annotator
scoreCoefficientsEvaluation

Score Coefficient Evaluation
molecular_formula_library_generator

Molecular Formula Database Producer
molecular_formula_elements_filter

molecular_formula_elements_filter
molecular_formula_annotator

Molecular Formula Annotator
identificationScoreCalculator

Multiplicative Identification Score for the IDSL.UFA pipeline
ionization_pathway_deconvoluter

Ionization Pathway Deconvoluter
isotopic_profile_calculator

Isotopic Profile Calculator
scoreCoefficientsOptimization

Coefficients Score Optimization
scoreCoefficientsReplicate

Zero Score Function
molecular_formula_library_search

Molecular Formula Library Search
UFA_formula_source_xlsxAnalyzer

UFA Formula Source xlsxAnalyzer
UFA_enumerated_chemical_space_xlsxAnalyzer

IPDBs from UFA Enumerated Chemical Space (ECS) xlsx Analyzer
UFA_enumerated_chemical_space

IPDBs from UFA Enumerated Chemical Space (ECS) approach
UFA_formula_source

IPDB from a Molecular Formulas Source
UFA_score_function_optimization

UFA Score Coefficient Workflow
UFA_IPdbMerger

UFA IPDB Merger
UFA_locate_regex

UFA Locate regex
UFA_score_function_optimization_xlsxAnalyzer

UFA Score Optimization xlsx Analyzer
UFA_PubChem_formula_extraction

UFA PubChem Formula Extraction