Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

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Documentation for package ‘tmod’ version 0.50.13

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

tmod-package	Transcriptional Module Analysis
as_tmodGS	S3 class for tmod gene set collections
cell_signatures	Cell type signatures
check_tmod_gs	Check an object of class tmodGS
Egambia	Gene expression in TB patients and Healthy controls
EgambiaResults	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
filterGS	Filter by genes belonging to a gene set from a data frame
getGenes	Get genes belonging to a gene set
getModuleMembers	Return the contents of a gene set
ggEvidencePlot	Create an evidence plot for a module (ggplot2 version)
ggPanelplot	Create a tmod panel plot using ggplot
hgEnrichmentPlot	Create a visualisation of enrichment
length.tmodGS	S3 class for tmod gene set collections
makeTmod	S3 class for tmod gene set collections
makeTmodFromDataFrame	Convert a data frame to a tmod object
makeTmodGS	S3 class for tmod gene set collections
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
pcaplot	Plot a PCA object returned by prcomp
print.tmodGS	S3 class for tmod gene set collections
pvalEffectPlot	Create an effect size / p-value plot
showGene	A combined beeswarm / boxplot
showModule	Filter by genes belonging to a gene set 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-data	Default gene expression module data
tmod2DataFrame	Convert a tmod module set into a data frame
tmod2tmodGS	Convert the old tmod objects to the tmodGS objects
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
tmodZtest	Perform a statistical test of module expression
tmod_ids	Query and set IDs of gene sets in a tmodGS object
tmod_ids<-	Query and set IDs of gene sets in a tmodGS object
tmod_titles	Query and set IDs of gene sets in a tmodGS object
tmod_titles<-	Query and set IDs of gene sets in a tmodGS object
upset	Upset plot
vaccination	Transcriptomic responses to vaccination
[.tmod	S3 class for tmod gene set collections
[.tmodGS	S3 class for tmod gene set collections