Man pages for hhabra/metabCombiner
Method for Combining LC-MS Metabolomics Feature Measurements
| adductdata | Retrieve Adduct Annotations |
| adjustData | Process and Filter Metabolomics Feature Lists |
| batchCombine | Stepwise Multi-batch LC-MS Alignment |
| calcScores | Compute Feature Similarity Scores |
| calcScoresParam | List calcScores Defaults |
| combineData | Obtain All Feature Data |
| combinedTable | Obtain Feature Alignment Report |
| combinerCheck | Obtain Errors for metabCombiner Object Checks |
| crossValFit | Cross Validation for Model Fits |
| datasets | Obtain Dataset IDs |
| detectFields | Detect metabData Input Columns |
| evaluateParams | Evaluate Similarity Score Parameters |
| featdata | Obtain Feature Metadata |
| filterAnchors | Filter Outlier Ordered Pairs |
| filtered | Retrieve Filtered Features |
| filterRT | Filter Features by Retention Time Range |
| fit_gam | Fit RT Projection Model With GAMs |
| fitgamParam | List fit_gam Defaults |
| fit_loess | Fit RT Projection Model With LOESS |
| fitloessParam | List fitLoess Defaults |
| getAnchors | Get Ordered Retention Time Pairs |
| getCoefficients | Obtain Last-Used Score Coefficients |
| getData | Get Processed Dataset |
| getExtra | Get Extra Data Column Names |
| getModel | Get Fitted RT Model |
| getSamples | Get Sample Names From metabCombiner or metabData Object |
| getStats | Get Object Statistics |
| iddata | Retrieve Feature Identities |
| identityAnchorSelection | Select Matching Ids as Anchors |
| isCombinedTable | Determine 'combinedTable' Validity |
| isMetabCombiner | Determine if object is a valid metabCombiner object |
| isMetabData | Determine validity of input metabData object |
| iterativeAnchorSelection | Iterative Selection of Ordered Pairs |
| labelRows | Annotate and Remove Report Rows |
| labelRowsParam | List labelRows & reduceTable Defaults |
| metabBatches | Three LC-MS Metabolomics Batch Datasets |
| metabCombine | metabCombiner Wrapper Function |
| metabCombiner | Form a metabCombiner object. |
| metabCombiner-class | 'metabCombiner' Combined Metabolomics Dataset Class |
| metabData | Constructor for the metabData object. |
| metabData-class | 'metabData' Single Metabolomics Dataset Class |
| mzdata | Retrieve m/z Values |
| mzFit | Compute m/z Shift Model |
| mzfitParam | Parameterize m/z Shift Model |
| mzGroup | Binning of mass spectral features in m/z dimension |
| nonmatched | Get Nonmatched Features |
| objective | Weight Parameter Objective Function |
| opts.duplicate | Duplicate Feature Detection Parameters |
| plasma20 | 20 minute LC-MS Analysis of Human Plasma |
| plasma30 | 30 minute LC-MS Analysis of Human Plasma |
| plot_fit | Plot metabCombiner Fits |
| Qdata | Retrieve Relative Abundance Values |
| resolveRows | Resolve Conflicting Alignment Subgroups |
| rtdata | Retrieve Retention Time Values |
| scorePairs | Calculate Pairwise Alignment Scores |
| selectAnchors | Select Anchors for Nonlinear RT Model |
| selectAnchorsParam | List selectAnchors Defaults |
| updateTables | Update 'metabCombiner' Objects |
| write2file | Print metabCombiner Report to File. |
| x | Obtain x & y Data Identifiers |
