Feature Set Enrichment Analysis for Metabolomics and Transcriptomics


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Documentation for package ‘tmod’ version 0.46.2

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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
vaccination Transcriptomic responses to vaccination
[-method Shows the tmod object