Normalization methods | Getting started | Examples
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-4.7)crmn_0.0.21.zip(r-4.6)crmn_0.0.21.zip(r-4.5)
crmn_0.0.21.tgz(r-4.6-any)crmn_0.0.21.tgz(r-4.5-any)
crmn_0.0.21.tar.gz(r-4.7-any)crmn_0.0.21.tar.gz(r-4.6-any)
crmn_0.0.21.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
crmn/json (API)
| # 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
Datasets:
- mix - Dilution mixture dataset.
Last updated from:5ba8389073. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 117 | ||
| source / vignettes | OK | 146 | ||
| linux-release-x86_64 | NOTE | 113 | ||
| macos-release-arm64 | NOTE | 149 | ||
| macos-oldrel-arm64 | NOTE | 198 | ||
| windows-devel | NOTE | 85 | ||
| windows-release | NOTE | 74 | ||
| windows-oldrel | NOTE | 91 | ||
| wasm-release | OK | 89 |
Exports:analytesdropunusedlevelsmakeXmethodmexprsmexprs<-modelnormalizenormFitnormPredsFitshowstandardsstandardsFitstandardsPredweightnorm
Dependencies:BiobaseBiocGenericsgenericsMASSpcaMethodsRcpp
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 |
