Man pages for lianos/multiGSEA
A unified interface to a plethora of gene set enrichment analysis methods

addGeneSetMetadataAdd metadata at the geneset level.
all.equal.GeneSetDbChecks equality (feature parity) between GeneSetDb objects
annotateGeneSetMembershipAnnotates rows of a data.frame with geneset membership from a...
append-GeneSetDb-ANY-methodAppends two GeneSetDb objects togethter.
calculateIndividualLogFCUtility function to run limma differential expression...
collectionMetadataGene Set Collection Metadata
conform(Re)-map geneset IDs to the rows in an expression object.
conversionConvert a GeneSetDb to other formats.
corplotPlots the correlation among the columns of a numeric matrix.
do.fgseaRuns GSEA on a pre-ranked list of differential expression...
do.goseqPerforms goseq analysis significance of gene set membership.
do.hyperGeometricTestPerforms a hypergeometric test for significance of gene set...
eigenWeightedMeanSingle sample gene set score by a weighted average of the...
examplesFunctions that load data for use in examples and testing.
failWithUtility function to try and fail with grace.
featureIdMapFetch the featureIdMap for a 'GeneSetDb'
featureIdsReturns the relevant featureIds for a given geneset.
geneSetFetches information for a gene set
GeneSetDb-classA container for geneset definitions.
geneSetsFetch the active (or all) gene sets from a GeneSetDb or...
geneSetsStatsSummarizes useful statistics per gene set from a...
geneSetSummaryByGenesSummarize geneset:feature relationships for specified set of...
getHousekeepingGeneSetDbRetrieves a housekeeping GeneSetDb for a given species
getPantherGeneSetDbGet pathways/GOslim information from PANTHER.db Biocondcutor...
getReactomeGeneSetDbRetrieve annotations from reactome.db
goseqPerform goseq Enrichment tests across a GeneSetDb.
gsdScoreSingle sample geneset score using SVD based eigengene value...
gskeyConverts collection,name combination to key for geneset
hasGeneSetCheck to see if the GeneSetDb has a collection,name GeneSet...
hasGeneSetCollectionCheck if a collection exists in the 'GeneSetDb'
hyperGeometricTestPerform Hypergeometric Enrichment tests across a GeneSetDb.
incidenceMatrixCreates a 1/0 matrix to indicate geneset membership to target...
iplotVisualize gene level behavior of genes within a geneset...
is.activeInterrogate "active" status of a given geneset.
logFCExtract the individual fold changes statistics for elements...
mgheatmapCreates a "geneset smart" ComplexHeatmap::Heatmap
msgUtility function to cat a message to stderr (by default)
MSigDBFetches a 'GeneSetDb' from geneset collections defined in...
multiGSEAPerforms a plethora of GSEA analyses over a contrast of...
multiGSEA.methodsLists the supported GSEA methods by multiGSEA
MultiGSEAResultA MultiGSEAResult object holds the results from a multiGSEA...
MultiGSEAResult-utilitiesFetches the GeneSetDb from MultiGSEAResult
p.matrixAssembles a matrix of nominal or adjusted pvalues from a...
rename_rowsSmartly/easily rename the rows of an object.
resultsInterrogate the results of a multiGSEA analysis stored in a...
scoreSingleSamplesGenerates single sample gene set scores across a datasets by...
ssGSEA.normalizeNormalize a vector of ssGSEA scores in the ssGSEA way.
sub-GeneSetDb-ANY-ANY-ANY-methodSubset whole genesets from a GeneSetDb
subsetByFeaturesSubset a GeneSetDb to only include geneSets with specified...
subset.GeneSetDbSubset GeneSetDb to only include specified genesets.
summarizedSummarizes different results into tabular form
validateInputsValidate the input objects to a GSEA call.
volcanoPlotCreate an interactive volcano plot
volcanoStatsTableExtracts x and y axis values from objects to create input for...
zScoreCalculate single sample geneset score by average z-score...
ztransformPvaluesZ-tranfsorm a vector of pvalues
lianos/multiGSEA documentation built on April 10, 2019, 8:38 p.m.