Method for Combining LC-MS Metabolomics Feature Measurements

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Documentation for package ‘metabCombiner’ version 1.15.2

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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