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)massSpectrometryR_0.6.5.zip(r-4.6)massSpectrometryR_0.6.5.zip(r-4.5)
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✨
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:

mass-spectrometry proteomics openjdk

2.40 score 1 scripts 40 exports 26 dependencies

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

Target	Result	Time
linux-devel-x86_64	OK	151
source / vignettes	OK	168
linux-release-x86_64	OK	139
macos-release-arm64	OK	182
macos-oldrel-arm64	OK	144
windows-devel	OK	95
windows-release	OK	87
windows-oldrel	OK	95
wasm-release	OK	120

Exports:%f-%%f+%addFormulas addListFormulas aminoAcidModifications aminoAcidResidues calculate.Measured.mz calculate.ppm calculate.Reference.mz chemicals digest electronFormula elements elementsAverage elementsInFormula elementsInFormulas elementsMonoisotopic emptyFormula formulaString formulaToMass massToMz massToMzH modifications mzHToMass mzToMass pdToFormula peptide peptideCount peptideFormula peptideFragments peptideMzH protonFormula rcdkFormula removeZeros sortFormula stringFormula stringToFormula subtractFormulas validFormula waterFormula

Dependencies:cli dplyr enviPat fingerprint generics glue iterators itertools lifecycle magrittr pillar pkgconfig png purrr R6 rcdk rcdklibs rJava rlang stringi stringr tibble tidyselect utf8 vctrs withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 elements	addFormulas
Add up a list of formulas	addListFormulas
R6 Class representing a set of amino acids	aminoAcidClass
Returns a pre-defined object which contains info on some common amino acid modifications	aminoAcidModifications
Generates a pre-defined object which contains info on 'normal' amino acid residues	aminoAcidResidues
calculate.Measured.mz	calculate.Measured.mz
calculate.ppm	calculate.ppm
calculate.Reference.mz	calculate.Reference.mz
R6 Class representing a set of chemicals	chemicals
Digests a sequence and returns	digest
generates a pre-defined formula for electron	electronFormula
R6 Class representing a set of elements	elements
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
elementsInFormula	elementsInFormula
Combine elements present in 2 separate formulas	elementsInFormulas
generates a pre-defined R6 elements object which contains info on elements, mass values are mono isotopic	elementsMonoisotopic
generates an empty pre-defined formula	emptyFormula
Translates regular formula format into a character vector, eg C6H12O6	formulaString
calculates the neutral mono-isotopic mass of a formula	formulaToMass
Calculates the m/z value of a charged/adducted ion	massToMz
Calculates the m/z value of a protonated ion (positive ESI)	massToMzH
R6 Class representing a set of modifications for the aminoacids in peptides	modifications
calculates the mass of the molecule in an ion (M+xH)x+	mzHToMass
calculates the mass of the molecule in an ion	mzToMass
translates a proteome Discoverer (Thermo Scientific) elements formula string to a formula as used by this package	pdToFormula
R6 Class representing a (single) peptide	peptide
counts the occurence of a amino acid (sequence) in another amino acid sequence	peptideCount
peptideFormula	peptideFormula
Generates a pre-defined (incomplete) table of names of fragments for the ions resulting when fragmenting a peptide in MS	peptideFragments
peptideMzH	peptideMzH
generates a pre-defined formula for proton	protonFormula
translates an cdkFormula object to a 'regular' formula format	rcdkFormula
removeZeros	removeZeros
sortFormula	sortFormula
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 elements	subtractFormulas
checks if formula is valid	validFormula
generates a pre-defined formula for water	waterFormula