MWASTools: an integrated pipeline to perform metabolome-wide association studies

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Documentation for package ‘MWASTools’ version 1.32.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

CV_filter	Filter metabolic data by CV
JBA_binning	Binning of pJRES spectra
JBA_corDistribution	Setting the ct threshold for JBA
JBA_plotBins	Visualization of JBA bins
KEGG_metabolic_paths	KEGG human metabolic pathways
metabo_SE	NMR plasma metabolic profiles dataset
MS_data	Simulated LC-MS features
MWAS_barplot	Visualize MWAS results in a bar plot
MWAS_bootstrapping	MWAS bootstrap resampling
MWAS_filter	Filter MWAS results by p-value and/or CV
MWAS_heatmap	Visualize MWAS results as a multiple-phenotype heatmap
MWAS_KEGG_network	Build a KEGG-based metabolic network
MWAS_KEGG_pathways	Map metabolites into KEGG pathways
MWAS_KEGG_shortestpaths	Build a shortest-path metabolic subnetwork
MWAS_network	Visualize MWAS results in a correlation-based metabolic network
MWAS_scatterplotMS	Visualize MWAS results in MS-based scatter plot
MWAS_skylineNMR	Visualize MWAS results in an NMR-skyline plot
MWAS_stats	Metabolome-Wide Associations
MWAS_SummarizedExperiment	Create a SummarizeExperiment object
plot_spectraNMR	Plot NMR spectra
QC_CV	Calculate coefficients of variation
QC_CV_scatterplot	Plot MS-based scatter plot colored based on CV
QC_CV_specNMR	Plot NMR spectrum colored based on CV
QC_PCA	Principal Component Analysis
QC_PCA_scoreplot	PCA score plot
STOCSY_NMR	Statistical Total Correlation Spectroscopy - Academic use only
targetMetabo_SE	Target NMR metabolites dataset