Package: massSpectrometryR 0.3.0

massSpectrometryR: massSpectrometryR

Provides calculations, plotting etc for chemistry & mass spectrometry.

Authors:Ben Bruyneel <[email protected]>

massSpectrometryR_0.3.0.tar.gz
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massSpectrometryR.pdf |massSpectrometryR.html✨
massSpectrometryR/json (API)

# Install 'massSpectrometryR' in R:
install.packages('massSpectrometryR', repos = c('https://benbruyneel.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/benbruyneel/massspectrometryr/issues

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On CRAN:

mass-spectrometryproteomics

1.70 score 1 scripts 37 exports 27 dependencies

Last updated 2 months agofrom:066d41a966. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-winERROROct 26 2024
R-4.5-linuxERROROct 26 2024
R-4.4-winERROROct 26 2024
R-4.4-macERROROct 26 2024
R-4.3-winERROROct 26 2024
R-4.3-macERROROct 26 2024

Exports:%f-%%f+%addFormulasaddListFormulasaminoAcidModificationsaminoAcidResidueschemicalsdigestelectronFormulaelementselementsAverageelementsInFormulaelementsInFormulaselementsMonoisotopicemptyFormulaformulaStringformulaToMassmassToMzmassToMzHmodificationsmzHToMassmzToMasspdToFormulapeptidepeptideCountpeptideFormulapeptideFragmentspeptideMzHprotonFormularcdkFormularemoveZerossortFormulastringFormulastringToFormulasubtractFormulasvalidFormulawaterFormula

Dependencies:clidplyrenviPatfansifingerprintgenericsglueiteratorsitertoolslifecyclemagrittrpillarpkgconfigpngpurrrR6rcdkrcdklibsrJavarlangstringistringrtibbletidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
custom operator for subtracting formulas from one another, to make calculating with formulas a little more clear%f-%
custom operator for adding up formulas, to make calculating with formulas a little more clear%f+%
Adding up two formulas, taking into account possible differing elementsaddFormulas
Add up a list of formulasaddListFormulas
R6 Class representing a set of amino acidsaminoAcidClass
Returns a pre-defined object which contains info on some common amino acid modificationsaminoAcidModifications
Generates a pre-defined object which contains info on 'normal' amino acid residuesaminoAcidResidues
R6 Class representing a set of chemicalschemicals
Digests a sequence and returnsdigest
generates a pre-defined formula for electronelectronFormula
R6 Class representing a set of elementselements
generates a pre-defined object which contains info on elements, mass values are average masses (weighted mean mass of elements based on their natural occurence)elementsAverage
elementsInFormulaelementsInFormula
Combine elements present in 2 separate formulaselementsInFormulas
generates a pre-defined R6 elements object which contains info on elements, mass values are mono isotopicelementsMonoisotopic
generates an empty pre-defined formulaemptyFormula
Translates regular formula format into a character vector, eg C6H12O6formulaString
calculates the neutral mono-isotopic mass of a formulaformulaToMass
Calculates the m/z value of a charged/adducted ionmassToMz
Calculates the m/z value of a protonated ion (positive ESI)massToMzH
R6 Class representing a set of modifications for the aminoacids in peptidesmodifications
calculates the mass of the molecule in an ion (M+xH)x+mzHToMass
calculates the mass of the molecule in an ionmzToMass
translates a proteome Discoverer (Thermo Scientific) elements formula string to a formula as used by this packagepdToFormula
R6 Class representing a (single) peptidepeptide
counts the occurence of a amino acid (sequence) in another amino acid sequencepeptideCount
peptideFormulapeptideFormula
Generates a pre-defined (incomplete) table of names of fragments for the ions resulting when fragmenting a peptide in MSpeptideFragments
peptideMzHpeptideMzH
generates a pre-defined formula for protonprotonFormula
translates an cdkFormula object to a 'regular' formula formatrcdkFormula
removeZerosremoveZeros
sortFormulasortFormula
Translates a character vector formula, eg 'C6H12O6' to a regular formula c(C=6, H=12, O=6)stringFormula
Translates a character vector formula, eg 'C6H12O6' to a regular formula c(C=6, H=12, O=6)stringToFormula
subtracting one formula from another, taking into account possible differing elementssubtractFormulas
checks if formula is validvalidFormula
generates a pre-defined formula for waterwaterFormula