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

## Documentation for package ‘MWASTools’ version 1.4.0

- 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