Package index • sparrow

All functions
`GeneSetDb()`	A container for geneset definitions.
`geneSetDb()`	Fetches the GeneSetDb from SparrowResult
`SparrowResult-class` `.SparrowResult` `SparrowResult`	A SparrowResult object holds the results from a sparrow::seas() 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
`calculateIndividualLogFC()`	Utility function to run limma differential expression analysis
`collectionMetadata()` `geneSetURL()` `featureIdType()` `featureIdType<-`() `addCollectionMetadata()`	Gene Set Collection Metadata
`combine(<GeneSetDb>,<GeneSetDb>)`	Combines two GeneSetDb objects together
`combine(<SparrowResult>,<SparrowResult>)`	Combines two SparrowResult objects together.
`conform()` `unconform()` `is.conformed()`	(Re)-map geneset IDs to the rows in an expression object.
`as.data.table(<GeneSetDb>)` `as.data.frame(<GeneSetDb>)`	Convert a GeneSetDb to other formats.
`convertIdentifiers()`	Converts internal feature identifiers in a GeneSetDb to a set of new ones.
`corplot()`	Plots the correlation among the columns of a numeric matrix.
`eigenWeightedMean()`	Single sample gene set score by a weighted average of the genes in geneset
`exampleExpressionSet()` `exampleGeneSets()` `exampleGeneSetDb()` `exampleBiocSet()` `exampleGeneSetDF()` `exampleSparrowResult()` `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
`geneSetCollectionURLfunction()` `geneSetCollectionURLfunction<-`()	Get/set the gene set collection url function for a geneset collection
`geneSetSummaryByGenes()`	Summarize geneset:feature relationships for specified set of features
`geneSets()` `length(<GeneSetDb>)` `nrow(<GeneSetDb>)`	Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult
`geneSetsStats()`	Summarizes useful statistics per gene set from a SparrowResult
`getKeggCollection()` `getKeggGeneSetDb()`	Retrieves the KEGG gene set collection via its REST API
`getMSigCollection()` `getMSigGeneSetDb()`	Fetches gene set collections from the moleular signature database (MSigDB)
`getPantherCollection()` `getPantherGeneSetDb()`	Get pathways/GOslim collections from PANTHER.db Biocondcutor package.
`getReactomeCollection()` `getReactomeGeneSetDb()`	Retrieve gene set collections from 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.
`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)
`ora()` `plot_ora_bias()`	Performs an overrepresentation analysis, (optionally) accounting for bias.
`p.matrix()`	Assembles a matrix of nominal or adjusted pvalues from a sparrow::seas result
`randomGeneSetDb()`	Generates a fake GeneSetDb by sampling from features in a seas input.
`renameCollections()`	Rename the collections in a GeneSetDb
`renameRows()`	Smartly/easily rename the rows of an object.
`resultNames()` `result()` `results()` `tabulateResults()`	Interrogate the results of a sparrow::seas analysis stored in a SparrowResult
`scale_rows()`	Centers and scales the rows of a numeric matrix.
`scoreSingleSamples()`	Generates single sample gene set scores across a datasets by many methods
`seas()`	Performs a plethora of set enrichment analyses over varied inputs.
`sparrow_methods()`	Lists the supported GSEA methods by sparrow
`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.
`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

Reference

All functions