Function reference • multiGSEA

All functions
`GeneSetDb()`	A container for geneset definitions.
`geneSetDb()`	Fetches the GeneSetDb from MultiGSEAResult
`MultiGSEAResult-class`	A MultiGSEAResult object holds the results from a multiGSEA call.
`addGeneSetMetadata()`	Add metadata at the geneset level.
`all.equal(<GeneSetDb>)`	Checks equality (feature parity) between GeneSetDb objects
`annotateGeneSetMembership()`	Annotates rows of a data.frame with geneset membership from a GeneSetDb
`append(<GeneSetDb>,<ANY>)`	Appends two GeneSetDb objects togethter.
`calculateIndividualLogFC()`	Utility function to run limma differential expression analysis
`collectionMetadata()` `geneSetURL()` `geneSetCollectionURLfunction()` `geneSetCollectionURLfunction<-`() `featureIdType()` `featureIdType<-`() `org()` `org<-`() `addCollectionMetadata()`	Gene Set Collection Metadata
`combine(<GeneSetDb>,<GeneSetDb>)`	Combines two GeneSetDb objects together
`combine(<MultiGSEAResult>,<MultiGSEAResult>)`	Combines two MultiGSEAResult objects together.
`conform()` `unconform()` `is.conformed()`	(Re)-map geneset IDs to the rows in an expression object.
`as.data.frame(<GeneSetDb>)` `as.list(<GeneSetDb>)`	Convert a GeneSetDb to other formats.
`corplot()`	Plots the correlation among the columns of a numeric matrix.
`do.fgsea()`	Runs GSEA on a pre-ranked list of differential expression statistcis with fgsea
`do.goseq()`	Performs goseq analysis significance of gene set membership.
`eigenWeightedMean()`	Single sample gene set score by a weighted average of the genes in geneset
`exampleExpressionSet()` `exampleGeneSets()` `exampleGeneSetDb()` `exampleGeneSetDF()` `exampleMultiGSEAResult()` `exampleDgeResult()`	Functions that load data for use in examples and testing.
`failWith()`	Utility function to try and fail with grace.
`featureIdMap()`	Fetch the featureIdMap for a `GeneSetDb`
`featureIds()`	Returns the relevant featureIds for a given geneset.
`geneSet()`	Fetches information for a gene set
`geneSetSummaryByGenes()`	Summarize geneset:feature relationships for specified set of features
`geneSets()`	Fetch the active (or all) gene sets from a GeneSetDb or MultiGSEAResult
`geneSetsStats()`	Summarizes useful statistics per gene set from a MultiGSEAResult
`getHousekeepingGeneSetDb()`	Retrieves a housekeeping GeneSetDb for a given species
`getKeggGeneSetDb()`	Retrieves a GeneSetDb from KEGG's REST API
`getMSigGeneSetDb()`	Fetches a `GeneSetDb` from geneset collections defined in MSigDB.
`getPantherGeneSetDb()` `getGOslimGeneSetDb()`	Get pathways/GOslim information from PANTHER.db Biocondcutor package.
`getReactomeGeneSetDb()`	Retrieve annotations from reactome.db
`goseq()`	Perform goseq Enrichment tests across a GeneSetDb.
`gsdScore()`	Single sample geneset score using SVD based eigengene value per sample.
`encode_gskey()` `split_gskey()`	Converts collection,name combination to key for geneset
`hasGeneSet()`	Check to see if the GeneSetDb has a collection,name GeneSet defined
`hasGeneSetCollection()`	Check if a collection exists in the `GeneSetDb`
`incidenceMatrix()`	Creates a 1/0 matrix to indicate geneset membership to target object.
`iplot()`	Visualize gene level behavior of genes within a geneset across a contrast.
`is.active()`	Interrogate "active" status of a given geneset.
`load_id_xref()`	Load the mouse or human ensembl <-> entrez id maps.
`logFC()`	Extract the individual fold changes statistics for elements in the expression object.
`mgheatmap()`	Creates a "geneset smart" ComplexHeatmap::Heatmap
`mgheatmap2()`	Creates a "geneset smart" ComplexHeatmap::Heatmap
`msg()`	Utility function to cat a message to stderr (by default)
`multiGSEA()`	Performs a plethora of GSEA analyses over a contrast of interest.
`multiGSEA_methods()`	Lists the supported GSEA methods by multiGSEA
`ora()`	Performs an overrepresentation analysis, (optinally) accounting for bias.
`p.matrix()`	Assembles a matrix of nominal or adjusted pvalues from a multiGSEA result
`pcWeightedMean()`	Just like eigenWeightedMean but direct from PCA (no gsdscore)
`plot_ora_bias()`	Plots bias of coviarate to DE / selected status
`remap_identifiers()`	Converts the feature identifiers in a GeneSetDb to a set of new ones.
`rename_rows()`	Smartly/easily rename the rows of an object.
`resultNames()` `result()` `results()` `tabulateResults()`	Interrogate the results of a multiGSEA analysis stored in a MultiGSEAResult
`scale_rows()`	Centers and scales the rows of a numeric matrix.
`scoreSingleSamples()`	Generates single sample gene set scores across a datasets by many methods
`species_info()`	Match a species query to the regularized species info.
`ssGSEA.normalize()`	Normalize a vector of ssGSEA scores in the ssGSEA way.
`[`(<GeneSetDb>,<ANY>,<ANY>,<ANY>)	Subset whole genesets from a GeneSetDb
`subset(<GeneSetDb>)`	Subset GeneSetDb to only include specified genesets.
`subsetByFeatures()`	Subset a GeneSetDb to only include geneSets with specified features.
`summarized()`	Summarizes different results into tabular form
`validateInputs()`	Validate the input objects to a GSEA call.
`volcanoPlot()`	Create an interactive volcano plot
`volcanoStatsTable()`	Extracts x and y axis values from objects to create input for volcano plot
`zScore()`	Calculate single sample geneset score by average z-score method
`ztransformPvalues()`	Z-tranfsorm a vector of pvalues

Reference

All functions