Man pages for lianos/multiGSEA
A unified interface to a plethora of gene set enrichment analysis methods
| 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... |
| append-GeneSetDb-ANY-method | Appends two GeneSetDb objects togethter. |
| calculateIndividualLogFC | Utility function to run limma differential expression... |
| collectionMetadata | Gene Set Collection Metadata |
| combine-GeneSetDb-GeneSetDb-method | Combines two GeneSetDb objects together |
| combine-MultiGSEAResult-MultiGSEAResult-method | Combines two MultiGSEAResult objects together. |
| conform | (Re)-map geneset IDs to the rows in an expression object. |
| conversion | 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... |
| do.goseq | Performs goseq analysis significance of gene set membership. |
| 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 |
| 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... |
| 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... |
| getPantherGeneSetDb | Get pathways/GOslim information from PANTHER.db Biocondcutor... |
| getReactomeGeneSetDb | Retrieve annotations 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. |
| load_id_xref | Load the mouse or human ensembl <-> entrez id maps. |
| 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) |
| multiGSEA | Performs a plethora of GSEA analyses over a contrast of... |
| multiGSEA_methods | Lists the supported GSEA methods by multiGSEA |
| MultiGSEAResult | A MultiGSEAResult object holds the results from a multiGSEA... |
| MultiGSEAResult-utilities | Fetches the GeneSetDb from MultiGSEAResult |
| ora | Performs an overrepresentation analysis, (optinally)... |
| pcWeightedMean | Just like eigenWeightedMean but direct from PCA (no gsdscore) |
| plot_ora_bias | Plots bias of coviarate to DE / selected status |
| p.matrix | Assembles a matrix of nominal or adjusted pvalues from a... |
| remap_identifiers | Converts the feature identifiers in a GeneSetDb to a set of... |
| rename_rows | Smartly/easily rename the rows of an object. |
| results | Interrogate the results of a multiGSEA analysis stored in a... |
| scale_rows | Centers and scales the rows of a numeric matrix. |
| scoreSingleSamples | Generates single sample gene set scores across a datasets by... |
| 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. |
| 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... |
| zScore | Calculate single sample geneset score by average z-score... |
| ztransformPvalues | Z-tranfsorm a vector of pvalues |
