Package: MSclassifR 0.3.3

Alexandre Godmer

MSclassifR: Automated Classification of Mass Spectra

Functions to classify mass spectra in known categories, and to determine discriminant mass-over-charge values. It includes easy-to-use functions for pre-processing mass spectra, functions to determine discriminant mass-over-charge values (m/z) from a library of mass spectra corresponding to different categories, and functions to predict the category (species, phenotypes, etc.) associated to a mass spectrum from a list of selected mass-over-charge values. Three vignettes illustrating how to use the functions of this package from real data sets are also available online to help users: <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Ecrobiav3.html>, <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_Klebsiellav3.html> and <https://agodmer.github.io/MSclassifR_examples/Vignettes/Vignettemsclassifr_DAv3.html>.

Authors:Alexandre Godmer [aut, cre], Quentin Giai Gianetto [aut], Karen Druart [aut]

MSclassifR_0.3.3.tar.gz
MSclassifR_0.3.3.tar.gz(r-4.5-noble)MSclassifR_0.3.3.tar.gz(r-4.4-noble)
MSclassifR_0.3.3.tgz(r-4.4-emscripten)MSclassifR_0.3.3.tgz(r-4.3-emscripten)
MSclassifR.pdf |MSclassifR.html✨
MSclassifR/json (API)

# Install 'MSclassifR' in R:

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

Bug tracker:https://github.com/agodmer/msclassifr_examples/issues

Datasets:

CitrobacterRKImetadata - Metadata of mass spectra corresponding to the bacterial species _Citrobacter_ sp. from The Robert Koch-Institute (RKI) database of microbial MALDI-TOF mass spectra
CitrobacterRKIspectra - Mass spectra corresponding to the bacterial species _Citrobacter_ sp. from The Robert Koch-Institute (RKI) database of microbial MALDI-TOF mass spectra

8 exports 1 stars 0.00 score 204 dependencies 297 downloads

Last updated 1 years agofrom:341ff2b319. Checks:OK: 1 NOTE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 26 2024
R-4.5-linux	NOTE	Aug 26 2024

Exports:LogReg PeakDetection PlotSpectra PredictFastClass PredictLogReg SelectionVar SelectionVarStat SignalProcessing

Dependencies:abind automap backports base64enc BBmisc BH Biobase BiocGenerics BiocParallel bit bit64 boot broom car carData caret checkmate class classInt cli clipr clock codetools colorspace corpcor cowplot cp4p cpp11 crayon data.table DBI DEoptimR Deriv diagram digest doBy doParallel dplyr e1071 ellipse evaluate fansi farver FNN forcats foreach formatR futile.logger futile.options future future.apply fuzzyjoin geeM geepack generics geosphere ggformula ggplot2 ggrepel ggridges glmnet globals glue gower gridExtra gstat gtable hardhat haven highr hms igraph intervals ipred isoband iterators jsonlite KernSmooth kinship2 knitr labeling labelled lambda.r lattice lava lifecycle limma listenv lme4 lubridate magrittr MALDIquant MALDIquantForeign MALDIrppa MASS mathjaxr Matrix MatrixModels matrixStats MBA mclust MESS metap mgcv microbenchmark minqa mixOmics mltools mnormt ModelMetrics modelr mosaicCore multcomp multitaper multtest munsell mutoss mvtnorm nlme nloptr nnet numDeriv parallelly parallelMap pbkrtest performanceEstimation pillar pkgconfig plotrix plyr prettyunits pROC prodlim progress progressr proxy purrr qqconf quadprog quantreg qvalue R6 randomForest rARPACK rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readBrukerFlexData readMzXmlData readr recipes reshape reshape2 rlang robustbase rpart RSpectra s2 sandwich scales sf sftime shape signal sn snow sp spacetime SparseM SQUAREM stars statmod stringdist stringi stringr survival TFisher TH.data tibble tidyr tidyselect timechange timeDate tzdb UBL units utf8 vctrs viridisLite vita vroom VSURF waveslim withr wk xfun xgboost XML xts yaml zoo

Citation

Readme and manuals

Help Manual

Help page	Topics
Metadata of mass spectra corresponding to the bacterial species _Citrobacter_ sp. from The Robert Koch-Institute (RKI) database of microbial MALDI-TOF mass spectra	CitrobacterRKImetadata
Mass spectra corresponding to the bacterial species _Citrobacter_ sp. from The Robert Koch-Institute (RKI) database of microbial MALDI-TOF mass spectra	CitrobacterRKIspectra
Estimation of a multinomial regression to predict the category to which a mass spectrum belongs	LogReg
Automated classification of mass spectra	MSclassifR
Detection of peaks in 'MassSpectrum' objects.	PeakDetection
Plot mass spectra with detected peaks	PlotSpectra
Prediction of the category to which a mass spectrum belongs using linear regressions of mass spectra.	PredictFastClass
Prediction of the category to which a mass spectrum belongs from a multinomial logistic regression model	PredictLogReg
Variable selection using random forests, logistic regression methods or sparse partial least squares discriminant analysis (sPLS-DA).	SelectionVar
Variable selection using multiple statistical tests.	SelectionVarStat
Function performing post acquisition signal processing	SignalProcessing

Package: MSclassifR 0.3.3

MSclassifR: Automated Classification of Mass Spectra

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)