# Method for Combining LC-MS Metabolomics Feature Measurements

## Documentation for package ‘metabCombiner’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

adjustData | Process and Filter Metabolomics Feature Lists
calcScores | Compute Feature Similarity Scores
combinedTable | Obtain metabCombiner Feature Alignment Report
combinedTable-method | Obtain metabCombiner Feature Alignment Report
combinerCheck | Obtain Errors for metabCombiner Object Checks
crossValFit | Cross Validation for Model Fits
detectFields | Detect metabData Input Columns
evaluateParams | Evaluate Similarity Score Parameters
filterAnchors | Filter Outlier Ordered Pairs
filterRT | Filter Features by Retention Time
findDuplicates | Find and Remove Duplicate Features
fit_gam | Fit RT Projection Model With GAMs
fit_loess | Fit RT Projection Model With LOESS
formCombinedTable | Form Combiner Report Table
getAnchors | Get Ordered Retention Time Pairs
getAnchors-method | Get Ordered Retention Time Pairs
getCoefficients | Obtain Last-Used Score Coefficients
getCoefficients-method | Obtain Last-Used Score Coefficients
getData | Get Processed Dataset
getData-method | Get Processed Dataset
getExtra | Get Extra Data Column Names
getExtra-method | Get Extra Data Column Names
getModel | Get Fitted RT Model
getModel-method | Get Fitted RT Model
getSamples | Get Sample Names From metabCombiner or metabData Object
getSamples-method | Get Sample Names From metabCombiner or metabData Object
getStats | Get Object Statistics
getStats-method | Get Object Statistics
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
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
mzGroup | Binning of mass spectral features in m/z dimension
nonmatched | Get Nonmatched Features
nonmatched-method | Get Nonmatched Features
objective | Weight Parameter Objective Function
plasma20 | 20 minute Metabolomics Analysis of Human Plasma
plasma30 | 30 minute Metabolomics Analysis of Human Plasma
plot-method | Plot metabCombiner Fits
plot_fit | Plot metabCombiner Fits
scorePairs | Calculate Pairwise Alignment Scores
selectAnchors | Select Anchors for Nonlinear RT Model
write2file | Print metabCombiner Report to File.