Package: MetaboCoreUtils 1.13.0

Johannes Rainer

MetaboCoreUtils: Core Utils for Metabolomics Data

MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.

Authors:Johannes Rainer [aut, cre], Michael Witting [aut], Andrea Vicini [aut], Liesa Salzer [ctb], Sebastian Gibb [aut], Michael Stravs [ctb], Roger Gine [aut], Philippine Louail [aut]

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MetaboCoreUtils/json (API)
NEWS

# Install 'MetaboCoreUtils' in R:

install.packages('MetaboCoreUtils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rformassspectrometry/metabocoreutils/issues

On BioConductor:MetaboCoreUtils-1.13.0(bioc 3.20)MetaboCoreUtils-1.12.0(bioc 3.19)

bioconductor-package

34 exports 4.13 score 16 dependencies 30 dependents

Last updated 2 months agofrom:257c5ad5f0

Exports:addElements adductFormula adductNames adducts adjust_lm calculateKm calculateKmd calculateMass calculateRkmd containsElements convertMtime correctRindex countElements fit_lm formula2mz indexRtime internalStandardMixNames internalStandards isotopicSubstitutionMatrix isotopologues isRkmd mass2mz mclosest multiplyElements mz2mass pasteElements percentMissing rowBlank rowDratio rowPercentMissing rowRsd rsd standardizeFormula subtractElements

Dependencies:BH BiocGenerics BiocParallel clue cluster codetools cpp11 formatR futile.logger futile.options lambda.r MASS MsCoreUtils Rcpp S4Vectors snow

Core Utils for Metabolomics Data

Rendered fromMetaboCoreUtils.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-04-13
Started: 2021-01-25

Help page	Topics
Combine chemical formulae	addElements
Calculate a table of adduct (ionic) formulas	adductFormula
Retrieve names of supported adducts	adductNames adducts
Kendrick mass defects	calculateKendrickMass calculateKm calculateKmd calculateRkmd isRkmd
Calculate exact mass	calculateMass
Check if one formula is contained in another	containsElements
Convert migration times to effective mobility	convertMtime
2-point correction of RIs	correctRindex
Count elements in a chemical formula	countElements
Linear model-based normalization of abundance matrices	adjust_lm fit_lm
Calculate mass-to-charge ratio from a formula	formula2mz
Convert retention times to retention indices	indexRtime
Get names of internal standard mixes provided by the package	internalStandardMixNames
Get definitions for internal standards	internalStandards
Definitions of isotopic substitutions	isotopicSubstitutionMatrix
Identfying isotopologue peaks in MS data	isotopologues
Calculate mass-to-charge ratio	mass2mz
Extract closest values in a pairwise manner between two matrices	mclosest
Multiply chemical formulas by a scalar	multiplyElements
Calculate neutral mass	mz2mass
Create chemical formula from a named vector	pasteElements
Basic quality assessment functions for metabolomics	percentMissing quality_assessment rowBlank rowDratio rowPercentMissing rowRsd rsd
Standardize a chemical formula	standardizeFormula
subtract two chemical formula	subtractElements

Package: MetaboCoreUtils 1.13.0

MetaboCoreUtils: Core Utils for Metabolomics Data

Core Utils for Metabolomics Data

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