Man pages for lianos/sparrow
Take command of set enrichment analyses through a unified interface
| 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... |
| calculateIndividualLogFC | Utility function to run limma differential expression... |
| collectionMetadata | Gene Set Collection Metadata |
| combine-GeneSetDb-GeneSetDb-method | Combines two GeneSetDb objects together |
| combine-SparrowResult-SparrowResult-method | Combines two SparrowResult objects together. |
| conform | (Re)-map geneset IDs to the rows in an expression object. |
| conversion | Convert a GeneSetDb to other formats. |
| convertIdentifiers | Converts internal feature identifiers in a GeneSetDb to a set... |
| corplot | Plots the correlation among the columns of a numeric matrix. |
| eigenWeightedMean | Single sample gene set score by a weighted average of the... |
| examples | 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 | Get/set the gene set collection url function for a geneset... |
| GeneSetDb-class | A container for geneset definitions. |
| geneSets | Fetch the active (or all) gene sets from a GeneSetDb or... |
| geneSetsStats | Summarizes useful statistics per gene set from a... |
| geneSetSummaryByGenes | Summarize geneset:feature relationships for specified set of... |
| getKeggCollection | Retrieves the KEGG gene set collection via its REST API |
| getMSigCollection | Fetches gene set collections from the moleular signature... |
| getPantherCollection | Get pathways/GOslim collections from PANTHER.db Biocondcutor... |
| getReactomeCollection | 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... |
| gskey | Converts collection,name combination to key for geneset |
| hasGeneSet | Check to see if the GeneSetDb has a collection,name GeneSet... |
| hasGeneSetCollection | Check if a collection exists in the 'GeneSetDb' |
| incidenceMatrix | Creates a 1/0 matrix to indicate geneset membership to target... |
| iplot | Visualize gene level behavior of genes within a geneset... |
| is.active | Interrogate "active" status of a given geneset. |
| logFC | Extract the individual fold changes statistics for elements... |
| 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 | Performs an overrepresentation analysis, (optionally)... |
| p.matrix | Assembles a matrix of nominal or adjusted pvalues from a... |
| randomGeneSetDb | Generates a fake GeneSetDb by sampling from features in a... |
| renameCollections | Rename the collections in a GeneSetDb |
| renameRows | Smartly/easily rename the rows of an object. |
| results | Interrogate the results of a sparrow::seas analysis stored in... |
| scale_rows | Centers and scales the rows of a numeric matrix. |
| scoreSingleSamples | Generates single sample gene set scores across a datasets by... |
| seas | Performs a plethora of set enrichment analyses over varied... |
| sparrow_methods | Lists the supported GSEA methods by sparrow |
| SparrowResult | A SparrowResult object holds the results from a... |
| SparrowResult-utilities | Fetches the GeneSetDb from SparrowResult |
| species_info | Match a species query to the regularized species info. |
| ssGSEA.normalize | Normalize a vector of ssGSEA scores in the ssGSEA way. |
| sub-GeneSetDb-ANY-ANY-ANY-method | Subset whole genesets from a GeneSetDb |
| subsetByFeatures | Subset a GeneSetDb to only include geneSets with specified... |
| subset.GeneSetDb | Subset GeneSetDb to only include specified genesets. |
| 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... |
| zScore | Calculate single sample geneset score by average z-score... |
