# Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

## Documentation for package ‘tmod’ version 0.31

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

## Help Pages

tmod-package | Transcriptional Module Analysis
Egambia | Gene expression in TB patients and Healthy controls
evidencePlot | Create an evidence plot for a module
getGenes | Get genes belonging to a module
getModuleMembers | Return the contents of a module
hgEnrichmentPlot | Create a visualisation of enrichment
makeTmod | S4 class for tmod
modmetabo | Modules for metabolic profiling
pvalEffectPlot | Create an effect size / p-value plot
show | Shows the tmod object
show-method | Shows the tmod object
showGene | A combined beeswarm / boxplot
showModule | Select genes belonging to a module from a data frame
tbmprof | Modules for metabolic profiling
tmod | Default gene expression module data
tmod-class | S4 class for tmod
tmod-data | Default gene expression module data
tmodAUC | Calculate AUC
tmodCERNOtest | Perform a statistical test of module expression
tmodDecideTests | Count the Up- or Down-regulated genes per module
tmodHGtest | Perform a statistical test of module expression
tmodImportMSigDB | Import data from MSigDB
tmodLimmaDecideTests | Up- and down-regulated genes in modules based on limma object
tmodLimmaTest | Run tmod enrichment tests directly on a limma object
tmodLimmaTopTable | tmod's replacement for the limma topTable function
tmodPal | A selection of color palettes
tmodPanelPlot | Plot a summary of multiple tmod analyses
tmodPCA | PCA plot annotated with tmod
tmodSummary | Create a summary of multiple tmod analyses
tmodTagcloud | Tag cloud based on tmod results
tmodUtest | Perform a statistical test of module expression
[ | Shows the tmod object
[-method | Shows the tmod object