# Method for Combining LC-MS Metabolomics Feature Measurements

## Documentation for package ‘metabCombiner’ version 1.20.0

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

## Help Pages

adductData | Retrieve Adduct Annotations
adductData-method | 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
combineData-method | Obtain All Feature Data
combinedTable | Obtain Feature Alignment Report
combinedTable-method | Obtain Feature Alignment Report
combinerCheck | Obtain Errors for metabCombiner Object Checks
crossValFit | Cross Validation for Model Fits
datasets | Obtain Dataset IDs
datasets-method | Obtain Dataset IDs
detectFields | Detect metabData Input Columns
evaluateParams | Evaluate Similarity Score Parameters
featData | Obtain Feature Metadata
featData-method | Obtain Feature Metadata
filterAnchors | Filter Outlier Ordered Pairs
filtered | Retrieve Filtered Features
filtered-method | Retrieve Filtered Features
filterRT | Filter Features by Retention Time Range
fitgamParam | List fit_gam Defaults
fitloessParam | List fitLoess Defaults
fit_gam | Fit RT Projection Model With GAMs
fit_loess | Fit RT Projection Model With LOESS
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
idData | Retrieve Feature Identities
idData-method | 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
mzData-method | 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
nonmatched-method | 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-method | Plot metabCombiner Fits
plot_fit | Plot metabCombiner Fits
QData | Retrieve Relative Abundance Values
QData-method | Retrieve Relative Abundance Values
reduceTable | Annotate and Remove Report Rows
reduceTableParam | List labelRows & reduceTable Defaults
resolveRows | Resolve Conflicting Alignment Subgroups
rtData | Retrieve Retention Time Values
rtData-method | 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
x-method | Obtain x & y Data Identifiers
xy | Obtain x & y Data Identifiers
xy-method | Obtain x & y Data Identifiers
y | Obtain x & y Data Identifiers
y-method | Obtain x & y Data Identifiers