Method for Combining LC-MS Metabolomics Feature Measurements


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Documentation for package ‘metabCombiner’ version 1.0.1

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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.