Function reference • tmod

Gene set enrichment tests and analyses

tmodUtest() tmodGeneSetTest() tmodCERNOtest() tmodPLAGEtest() tmodZtest() tmodHGtest(): Perform a statistical test of module expression

tmodPCA(): PCA plot annotated with tmod

tmodSummary(): Create a summary of multiple tmod analyses

tmodLEA(): Leading Edge Analysis

tmodLEASummary(): Summary stats of a leading edge analysis

tmodDecideTests(): Count the Up- or Down-regulated genes per module

tmodLimmaTest(): Run tmod enrichment tests directly on a limma object

tmodLimmaDecideTests(): Up- and down-regulated genes in modules based on limma object

tmodLimmaTopTable(): tmod's replacement for the limma topTable function

tmodAUC(): Calculate AUC

Gene set (module) analysis

eigengene(): Calculate the eigengene of a module from a data set

modGroups(): Find group of modules

modOverlaps(): Calculate overlaps of the modules

modcors(): Module correlation

modjaccard(): Jaccard index for modules

Visualizations

ggPanelplot(): Create a tmod panel plot using ggplot

ggEvidencePlot(): Create an evidence plot for a module (ggplot2 version)

tmodPanelPlot(): Plot a summary of multiple tmod analyses

pvalEffectPlot(): Create an effect size / p-value plot

upset(): Upset plot

evidencePlot(): Create an evidence plot for a module

hgEnrichmentPlot(): Create a visualisation of enrichment

modCorPlot(): Plot a correlation heatmap for modules

showGene(): A combined beeswarm / boxplot

pcaplot(): Plot a PCA object returned by prcomp

tmodPal(): A selection of color palettes

tmodTagcloud(): Tag cloud based on tmod results

simplePie() simpleRug() simpleBoxpie(): Simple Pie Chart

Creating and manipulating gene sets (modules)

makeTmodGS() makeTmod() as_tmodGS() print(<tmodGS>) length(<tmodGS>) `[`(<tmodGS>) `[`(<tmod>): S3 class for tmod gene set collections

makeTmodFromDataFrame(): Convert a data frame to a tmod object

tmodImportMSigDB(): Import data from MSigDB

tmod2DataFrame(): Convert a tmod module set into a data frame

getGenes(): Get genes belonging to a gene set

getModuleMembers(): Return the contents of a gene set

filterGS() showModule(): Filter by genes belonging to a gene set from a data frame

tmod_ids() `tmod_ids<-`() tmod_titles() `tmod_titles<-`(): Query and set IDs of gene sets in a tmodGS object

tmod2tmodGS(): Convert the old tmod objects to the tmodGS objects

check_tmod_gs(): Check an object of class tmodGS

Data sets

tmod-data tmod: Default gene expression module data

modmetabo tbmprof: Modules for metabolic profiling

EgambiaResults Egambia: Gene expression in TB patients and Healthy controls

vaccination: Transcriptomic responses to vaccination

cell_signatures: Cell type signatures

General and package classes

tmod-package: Transcriptional Module Analysis