Package: MetaboCoreUtils 1.21.1

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], William Kumler [aut], Philippine Louail [aut], Gabriele Tomè [aut]

MetaboCoreUtils_1.21.1.tar.gz
MetaboCoreUtils_1.21.1.zip(r-4.7)MetaboCoreUtils_1.21.1.zip(r-4.6)MetaboCoreUtils_1.21.1.zip(r-4.5)
MetaboCoreUtils_1.21.1.tgz(r-4.6-any)MetaboCoreUtils_1.21.1.tgz(r-4.5-any)
MetaboCoreUtils_1.21.1.tar.gz(r-4.7-any)MetaboCoreUtils_1.21.1.tar.gz(r-4.6-any)
MetaboCoreUtils_1.21.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MetaboCoreUtils/json (API)

# 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-1.21.1(bioc 3.24)MetaboCoreUtils-1.20.1(bioc 3.23)

infrastructure metabolomics massspectrometry mass-spectrometry

10.22 score 9 stars 71 packages 95 scripts 3.3k downloads 42 exports 17 dependencies

Last updated from:1e25732196. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	142
linux-devel-x86_64	OK	201
source / vignettes	OK	202
linux-release-x86_64	OK	171
macos-release-arm64	OK	117
macos-oldrel-arm64	OK	138
windows-devel	OK	127
windows-release	OK	117
windows-oldrel	OK	113
wasm-release	OK	120

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

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

Core Utils for Metabolomics Data

Rendered fromMetaboCoreUtils.Rmdusingknitr::rmarkdown

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

Help page	Topics
Combine chemical formulae	addElements
Get the charge of an adduct	adductCharge
Calculate a table of adduct (ionic) formulas	adductFormula
Retrieve names of supported adducts	adductNames adducts
Peak shape quality: beta parameters	betaValues
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
Guess the source of names	guessSource
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
Get mapping vector between two software	nameMapping
Create chemical formula from a named vector	pasteElements
Basic quality assessment functions for metabolomics	percentMissing quality_assessment rowBlank rowDratio rowPercentMissing rowRsd rsd
Get supported software for name translation	softwareMapping
Get mapping schema for name translation	softwareMappingSchema
Standardize a chemical formula	standardizeFormula
Fix short-hand charge notation in adduct definition	standardizeSingleCharge
subtract two chemical formula	subtractElements
Translate names based on a provided mapping	translate

Package: MetaboCoreUtils 1.21.1

MetaboCoreUtils: Core Utils for Metabolomics Data

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)