Package: crmn 0.0.21
crmn: CCMN and Other Normalization Methods for Metabolomics Data
Implements the Cross-contribution Compensating Multiple standard Normalization (CCMN) method described in Redestig et al. (2009) Analytical Chemistry https://doi.org/10.1021/ac901143w and other normalization algorithms.
Authors:
crmn_0.0.21.tar.gz
crmn_0.0.21.zip(r-4.5)crmn_0.0.21.zip(r-4.4)crmn_0.0.21.zip(r-4.3)
crmn_0.0.21.tgz(r-4.4-any)crmn_0.0.21.tgz(r-4.3-any)
crmn_0.0.21.tar.gz(r-4.5-noble)crmn_0.0.21.tar.gz(r-4.4-noble)
crmn_0.0.21.tgz(r-4.4-emscripten)crmn_0.0.21.tgz(r-4.3-emscripten)
crmn.pdf |crmn.html✨
crmn/json (API)
NEWS
| # Install 'crmn' in R: |
| install.packages('crmn', repos = c('https://hredestig.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hredestig/crmn/issues
- mix - Dilution mixture dataset.
Last updated 5 years agofrom:5ba8389073. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | OK | Oct 30 2024 |
| R-4.3-mac | OK | Oct 30 2024 |
Exports:analytesdropunusedlevelsmakeXmethodmexprsmexprs<-modelnormalizenormFitnormPredsFitshowstandardsstandardsFitstandardsPredweightnorm
Dependencies:BiobaseBiocGenericsMASSpcaMethodsRcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Accessor for the analytes | analytes |
| Accessor for the analytes | analytes,ExpressionSet,missing-method analytes_eset |
| Accessor for the analytes | analytes,data.frame,logical-method analytes,matrix,logical-method analytes_other |
| CRMN | crmn-package crmn |
| Drop unused levels | dropunusedlevels |
| Make X | makeX makeX,ANY,matrix-method makeX,ExpressionSet,character-method makeX-methods |
| Accessor for the method | method method,nFit-method method-methods |
| Matrix safe accessor of expression slot | mexprs mexprs,ExpressionSet-method mexprs,matrix-method mexprs-methods |
| Accessor | mexprs-rep-methods mexprs<- mexprs<-,ExpressionSet,matrix-method mexprs<-,matrix,matrix-method |
| Dilution mixture dataset. | mix |
| Accessor for the model | model model,nFit-method model-methods |
| Normalization model | nFit nFit-class |
| Normalize a metabolomics dataset | normalize |
| Fit a normalization model | normFit |
| Predict for normalization | normPred |
| Muffle the pca function | pcaMuffle |
| Plot a statistics for CRMN normalization model | plot,nFit-method plot.nFit |
| Accessor for the standards model | sFit sFit,nFit-method sFit-method |
| Show method for nFit | show show,nFit-method |
| Show nfit | show_nfit |
| Accessor for the Internal Standards | standards |
| Accessor for the Internal Standards | standards,ExpressionSet,missing-method standards_eset |
| Accessor for the Internal Standards | standards,data.frame,logical-method standards,matrix,logical-method standards_other |
| Standards model | standardsFit |
| Predict effect for new data (or get fitted data) | standardsPred |
| Normalize by sample weight | weightnorm |
