Feature Set Enrichment Analysis for Metabolomics and Transcriptomics


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Documentation for package ‘tmod’ version 0.31

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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