Man pages for jasenfinch/metabolyseR
Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
| aggregate | Sample aggregation |
| analysis-accessors | 'AnalysisData' and 'Analysis' class accessors |
| Analysis-class | Analysis S4 class |
| analysisData | AnalysisData class constructor |
| AnalysisData-class | AnalysisData S4 class |
| analysisElements | Analysis elements |
| analysisParameters | Create an 'AnalysisParameters' S4 class object |
| AnalysisParameters-class | AnalysisParameters S4 class |
| anova | ANOVA |
| bind | Bind 'AnalysisData' objects by row |
| changeParameter | Change analysis parameters |
| cls | Sample meta information wrangling |
| correction | Batch/block correction |
| correlations | Feature correlation analysis |
| correlationsParameters | Correlations parameters |
| impute | Missing data imputation |
| io-parameters | Parse/export analysis parameters |
| keep | Keep samples, classes or features |
| linearRegression | Linear regression |
| mds | Multidimensional scaling (MDS) |
| metabolyse | Perform an analysis |
| modelling-accessors | Modelling accessor methods |
| modelling-parameters | Modelling parameters |
| occupancy | Calculate feature class occupancies |
| occupancyFilter | Feature occupancy filtering |
| parameters | Get or set analysis parameters |
| plotExplanatoryHeatmap | Heatmap plot of explantory features |
| plotFeature | Plot a feature |
| plotImportance | Plot feature importance |
| plotLDA | Principle Component - Linear Discriminant Analysis plot |
| plotMDS | Multidimensional scaling (MDS) plot |
| plotMetrics | Plot model performance metrics |
| plotOccupancy | Plot class occupancy distributions |
| plotPCA | Principle Component Analysis plot |
| plotROC | Plot receiver operator characteristic (ROC) curves |
| plotRSD | Plot RSD distributions |
| plotSupervisedRF | Supervised random forest MDS plot |
| plotTIC | Plot sample total ion counts |
| plotUnsupervisedRF | Unsupervised random forest MDS plot |
| predict | Predict random forest model responses |
| pre-treatment-parameters | Pre-treatment parameters |
| QC | Quality control (QC) sample treatments |
| randomForest | Random forest |
| RandomForest-class | RandomForest S4 class |
| reexports | Objects exported from other packages |
| remove | Remove samples, classes or features |
| roc | Receiver-operator characteristic (ROC) curves |
| rsd | Calculate feature relative standard deviations |
| split | Split an 'AnalysisData' object |
| transform | Scaling, transformation and normalisation methods |
| ttest | Welch's t-test |
| tune | Tune random forest parameters |
| Univariate-class | Univariate S4 class |
