Package: assignments 1.0.2

Jasen Finch

assignments: Molecular Formula Assignment For High Resolution ESI-MS Based Metabolomics Data

A molecular formula assignment approach for electrospray ionisation high resolution mass spectrometry based metabolomics data.

Authors:Jasen Finch [aut, cre]

assignments_1.0.2.tar.gz
assignments_1.0.2.zip(r-4.7)assignments_1.0.2.zip(r-4.6)assignments_1.0.2.zip(r-4.5)
assignments_1.0.2.tgz(r-4.6-any)assignments_1.0.2.tgz(r-4.5-any)
assignments_1.0.2.tar.gz(r-4.7-any)assignments_1.0.2.tar.gz(r-4.6-any)
assignments_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
assignments/json (API)

# Install 'assignments' in R:

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

Bug tracker:https://github.com/aberhrml/assignments/issues

Pkgdown/docs site:https://aberhrml.github.io

Datasets:

feature_data - Example feature data

On CRAN:

2.70 score 1 stars 3 scripts 50 exports 106 dependencies

Last updated from:e11cad4a03. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	319
source / vignettes	OK	333
linux-release-x86_64	OK	320
macos-release-arm64	OK	189
macos-oldrel-arm64	OK	186
windows-devel	OK	289
windows-release	OK	259
windows-oldrel	OK	287
wasm-release	OK	198

Exports:%>%addIsoAssign adductRules adductRules<-adducts adducts<-assignedData assignment assignmentParameters assignments assignMFs availableTechniques calcCorrelations calcRelationships component components correlations correlationsParameters correlationsParameters<-edges featureComponents featureData graph isotopeRules isotopeRules<-isotopes isotopes<-iterations limit limit<-maxM maxM<-MFrankThreshold MFrankThreshold<-nodes plan plotAdductDist plotComponent plotFeatureComponents plotSpectrum ppm ppm<-relationships summariseAssignments technique transformationAssign transformationRules transformationRules<-transformations transformations<-

Dependencies:backports base64enc broom bslib cachem checkmate class cli cluster codetools colorspace cpp11 crayon data.table digest doFuture doRNG dplyr e1071 evaluate farver fastmap fontawesome foreach foreign forestControl Formula fs furrr future future.apply generics ggdendro ggplot2 ggrepel ggthemes globals glue gridExtra gtable hardhat highr Hmisc htmlTable htmltools htmlwidgets igraph isoband iterators itertools jquerylib jsonlite knitr labeling lattice lifecycle listenv lubridate magrittr MASS Matrix memoise metabolyseR mime missForest mzAnnotation nnet parallelly patchwork pillar pkgconfig proxy purrr R6 randomForest ranger rappdirs rbibutils RColorBrewer Rcpp RcppEigen Rdpack rlang rmarkdown rngtools rpart rstudioapi S7 sass scales sparsevctrs stringi stringr tibble tidygraph tidyr tidyselect timechange tinytex utf8 vctrs viridisLite withr xfun yaml yardstick

assignments

Rendered fromassignments.Rmdusingknitr::rmarkdown

Last update: 2023-02-21
Started: 2023-02-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create an Assignment S4 class object	assignment assignment,Analysis,AssignmentParameters-method assignment,AnalysisData,AssignmentParameters-method assignment,tbl_df,AssignmentParameters-method
Assignment	Assignment-class
Assignment parameters	assignmentParameters
S4 class for assignment parameters	AssignmentParameters-class
Perform molecular formula assignment	assignMFs assignMFs,Analysis-method assignMFs,AnalysisData-method assignMFs,tbl_df-method
Available analytical techniques	availableTechniques
Molecular formula assignment methods	addIsoAssign addIsoAssign,Assignment-method calcCorrelations calcCorrelations,Assignment-method calcRelationships calcRelationships,Assignment-method transformationAssign transformationAssign,Assignment-method
Example feature data	feature_data
Assignment accessors	assignedData assignedData,Assignment-method assignments assignments,Assignment-method component component,Assignment-method components components,Assignment-method correlations correlations,Assignment-method featureComponents featureComponents,Assignment-method featureData featureData,Assignment-method graph graph,Assignment-method iterations iterations,Assignment-method relationships relationships,Assignment-method summariseAssignments summariseAssignments,Assignment-method
Extract graph attributes	edges nodes
Plot assignment results	plotAdductDist plotAdductDist,Assignment-method plotComponent plotComponent,Assignment-method plotFeatureComponents plotFeatureComponents,Assignment-method plotSpectrum plotSpectrum,Assignment-method
Parameter get and set methods	adductRules adductRules,AssignmentParameters-method adductRules<- adductRules<-,AssignmentParameters-method adducts adducts,AssignmentParameters-method adducts<- adducts<-,AssignmentParameters-method correlationsParameters correlationsParameters,AssignmentParameters-method correlationsParameters<- correlationsParameters<-,AssignmentParameters,list-method isotopeRules isotopeRules,AssignmentParameters-method isotopeRules<- isotopeRules<-,AssignmentParameters-method isotopes isotopes,AssignmentParameters-method isotopes<- isotopes<-,AssignmentParameters-method limit limit,AssignmentParameters-method limit<- limit<-,AssignmentParameters-method maxM maxM,AssignmentParameters-method maxM<- maxM<-,AssignmentParameters-method MFrankThreshold MFrankThreshold,AssignmentParameters-method MFrankThreshold<- MFrankThreshold<-,AssignmentParameters-method ppm ppm,AssignmentParameters-method ppm<- ppm<-,AssignmentParameters-method technique technique,AssignmentParameters-method transformationRules transformationRules,AssignmentParameters-method transformationRules<- transformationRules<-,AssignmentParameters-method transformations transformations,AssignmentParameters-method transformations<- transformations<-,AssignmentParameters-method