Package: metabCombiner 1.23.0

Hani Habra

metabCombiner: Method for Combining LC-MS Metabolomics Feature Measurements

This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

Authors:Hani Habra [aut, cre], Alla Karnovsky [ths]

# Install 'metabCombiner' in R:

install.packages('metabCombiner', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hhabra/metabcombiner/issues

Datasets:

metabBatches - Three LC-MS Metabolomics Batch Datasets
plasma20 - 20 minute LC-MS Analysis of Human Plasma
plasma30 - 30 minute LC-MS Analysis of Human Plasma

On BioConductor:metabCombiner-1.23.0(bioc 3.24)metabCombiner-1.22.0(bioc 3.23)

software massspectrometry metabolomics mass-spectrometry

5.85 score 13 stars 18 scripts 45 exports 77 dependencies

Last updated from:2467920618. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	185
linux-devel-arm64	NOTE	219
linux-devel-x86_64	NOTE	257
source / vignettes	OK	234
linux-release-arm64	NOTE	238
linux-release-x86_64	NOTE	250
macos-release-arm64	NOTE	142
macos-release-x86_64	NOTE	348
macos-oldrel-arm64	NOTE	126
macos-oldrel-x86_64	NOTE	303
windows-devel	NOTE	173
windows-release	NOTE	179
windows-oldrel	NOTE	207
wasm-release	OK	155

Exports:adductData batchCombine calcScores calcScoresParam combineData combinedTable datasets evaluateParams featData filtered fit_gam fit_loess fitgamParam fitloessParam getAnchors getCoefficients getData getExtra getModel getSamples getStats idData labelRows labelRowsParam metabCombine metabCombiner metabData mzData mzFit mzfitParam nonmatched opts.duplicate plot plot_fit QData reduceTable reduceTableParam rtData selectAnchors selectAnchorsParam updateTables write2file x xy y

Dependencies:BiocGenerics caret class cli clock codetools cpp11 data.table diagram digest dplyr e1071 farver foreach future future.apply generics ggplot2 globals glue gower gtable hardhat ipred isoband iterators KernSmooth labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix matrixStats mgcv ModelMetrics nlme nnet numDeriv parallelly pillar pkgconfig plyr pROC prodlim progressr proxy purrr R6 RColorBrewer Rcpp recipes reshape2 rlang rpart S4Vectors S7 scales shape sparsevctrs SQUAREM stringi stringr survival tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite withr

Combine LC-MS Metabolomics Datasets with metabCombiner

Rendered frommetabCombiner_vignette.Rmdusingknitr::rmarkdown

Last update: 2023-04-11
Started: 2020-06-01

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

Package: metabCombiner 1.23.0

metabCombiner: Method for Combining LC-MS Metabolomics Feature Measurements

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