# Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

## Documentation for package ‘tmod’ version 0.44

- 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
eigengene | Calculate the eigengene of a module from a data set
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
length | Shows the length of a tmod object
length-method | Shows the length of a tmod object
makeTmod | S4 class for tmod
makeTmodFromDataFrame | Convert a data frame to a tmod object
mbind | Bind two or more transcriptional module sets
modCorPlot | Plot a correlation heatmap for modules
modcors | Module correlation
modGroups | Find group of modules
modjaccard | Jaccard index for modules
modmetabo | Modules for metabolic profiling
modOverlaps | Calculate overlaps of the modules
mset2mtx | Convert between matrix representation of modules and tmod objects
mtx2mset | Convert between matrix representation of modules and tmod objects
pcaplot | Plot a PCA object returned by prcomp
pvalEffectPlot | Create an effect size / p-value plot
renameMods | Rename module IDs
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
simpleBoxpie | Simple Pie Chart
simplePie | Simple Pie Chart
simpleRug | Simple Pie Chart
tbmprof | Modules for metabolic profiling
tmod | Default gene expression module data
tmod-class | S4 class for tmod
tmod-data | Default gene expression module data
tmod2DataFrame | Convert a tmod module set into a data frame
tmodAUC | Calculate AUC
tmodCERNOtest | Perform a statistical test of module expression
tmodDecideTests | Count the Up- or Down-regulated genes per module
tmodGeneSetTest | Perform a statistical test of module expression
tmodHGtest | Perform a statistical test of module expression
tmodImportMSigDB | Import data from MSigDB
tmodLEA | Leading Edge Analysis
tmodLEASummary | Summary stats of a leading edge analysis
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
tmodPLAGEtest | Perform a statistical test of module expression
tmodSummary | Create a summary of multiple tmod analyses
tmodTagcloud | Tag cloud based on tmod results
tmodUtest | Perform a statistical test of module expression
tmodWZtest | Perform a statistical test of module expression
tmodZtest | Perform a statistical test of module expression
upset | Upset plot
[-method | Shows the tmod object