Package: massSpectrometryR 0.6.5

massSpectrometryR: massSpectrometryR

Provides calculations, plotting etc for chemistry & mass spectrometry.

Authors:Ben Bruyneel <[email protected]>

massSpectrometryR_0.6.5.tar.gz
massSpectrometryR_0.6.5.zip(r-4.7-any)massSpectrometryR_0.6.5.zip(r-4.6-any)massSpectrometryR_0.6.5.zip(r-4.5-any)
massSpectrometryR_0.6.5.tgz(r-4.6-any)massSpectrometryR_0.6.5.tgz(r-4.5-any)
massSpectrometryR_0.6.5.tar.gz(r-4.7-any)massSpectrometryR_0.6.5.tar.gz(r-4.6-any)
massSpectrometryR_0.6.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
massSpectrometryR/json (API)

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

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

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

On CRAN:

Conda:

mass-spectrometryproteomicsopenjdk

2.30 score 1 scripts 40 exports 26 dependencies

Last updated from:1c7d830426. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK179
source / vignettesOK192
linux-releaseOK135
macos-releaseOK98
macos-oldrelOK130
windows-develOK89
windows-releaseOK100
windows-oldrelOK92
wasm-releaseOK114

Exports:%f-%%f+%addFormulasaddListFormulasaminoAcidModificationsaminoAcidResiduescalculate.Measured.mzcalculate.ppmcalculate.Reference.mzchemicalsdigestelectronFormulaelementselementsAverageelementsInFormulaelementsInFormulaselementsMonoisotopicemptyFormulaformulaStringformulaToMassmassToMzmassToMzHmodificationsmzHToMassmzToMasspdToFormulapeptidepeptideCountpeptideFormulapeptideFragmentspeptideMzHprotonFormularcdkFormularemoveZerossortFormulastringFormulastringToFormulasubtractFormulasvalidFormulawaterFormula

Dependencies:clidplyrenviPatfingerprintgenericsglueiteratorsitertoolslifecyclemagrittrpillarpkgconfigpngpurrrR6rcdkrcdklibsrJavarlangstringistringrtibbletidyselectutf8vctrswithr

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
calculate.Measured.mzcalculate.Measured.mz
calculate.ppmcalculate.ppm
calculate.Reference.mzcalculate.Reference.mz
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