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


[Up] [Top]

Documentation for package ‘MWASTools’ version 1.10.0

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