Take command of set enrichment analyses through a unified interface

Documentation for package ‘sparrow’ version 1.15.0

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A C E F G H I L M N O P R S T U V Z misc

-- A --

addCollectionMetadata	Gene Set Collection Metadata
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
as.data.frame	Convert a GeneSetDb to other formats.
as.data.frame.GeneSetDb	Convert a GeneSetDb to other formats.
as.data.table	Convert a GeneSetDb to other formats.
as.data.table.GeneSetDb	Convert a GeneSetDb to other formats.
as.list	Convert a GeneSetDb to other formats.

-- C --

calculateIndividualLogFC	Utility function to run limma differential expression analysis
collectionMetadata	Gene Set Collection Metadata
collectionMetadata-method	Gene Set Collection Metadata
combine-method	Combines two GeneSetDb objects together
combine-method	Combines two SparrowResult objects together.
conform	(Re)-map geneset IDs to the rows in an expression object.
conform-method	(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 of new ones.
convertIdentifiers-method	Converts internal feature identifiers in a GeneSetDb to a set of new ones.
corplot	Plots the correlation among the columns of a numeric matrix.

-- E --

eigenWeightedMean	Single sample gene set score by a weighted average of the genes in geneset
encode_gskey	Converts collection,name combination to key for geneset
exampleBiocSet	Functions that load data for use in examples and testing.
exampleDgeResult	Functions that load data for use in examples and testing.
exampleExpressionSet	Functions that load data for use in examples and testing.
exampleGeneSetDb	Functions that load data for use in examples and testing.
exampleGeneSetDF	Functions that load data for use in examples and testing.
exampleGeneSets	Functions that load data for use in examples and testing.
exampleSparrowResult	Functions that load data for use in examples and testing.

-- F --

failWith	Utility function to try and fail with grace.
featureIdMap	Fetch the featureIdMap for a 'GeneSetDb'
featureIdMap-method	Fetch the featureIdMap for a 'GeneSetDb'
featureIds	Returns the relevant featureIds for a given geneset.
featureIds-method	Returns the relevant featureIds for a given geneset.
featureIdType	Gene Set Collection Metadata
featureIdType-method	Gene Set Collection Metadata
featureIdType<-	Gene Set Collection Metadata
featureIdType<--method	Gene Set Collection Metadata

-- G --

geneSet	Fetches information for a gene set
geneSet-method	Fetches information for a gene set
geneSetCollectionURLfunction	Get/set the gene set collection url function for a geneset collection
geneSetCollectionURLfunction-method	Get/set the gene set collection url function for a geneset collection
geneSetCollectionURLfunction<-	Get/set the gene set collection url function for a geneset collection
geneSetCollectionURLfunction<--method	Get/set the gene set collection url function for a geneset collection
GeneSetDb	A container for geneset definitions.
geneSetDb	Fetches the GeneSetDb from SparrowResult
GeneSetDb-class	A container for geneset definitions.
geneSets	Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult
geneSets-method	Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult
geneSetsStats	Summarizes useful statistics per gene set from a SparrowResult
geneSetSummaryByGenes	Summarize geneset:feature relationships for specified set of features
geneSetSummaryByGenes-method	Summarize geneset:feature relationships for specified set of features
geneSetURL	Gene Set Collection Metadata
geneSetURL-method	Gene Set Collection Metadata
getKeggCollection	Retrieves the KEGG gene set collection via its REST API
getKeggGeneSetDb	Retrieves the KEGG gene set collection via its REST API
getMSigCollection	Fetches gene set collections from the moleular signature database (MSigDB)
getMSigGeneSetDb	Fetches gene set collections from the moleular signature database (MSigDB)
getPantherCollection	Get pathways/GOslim collections from PANTHER.db Biocondcutor package.
getPantherGeneSetDb	Get pathways/GOslim collections from PANTHER.db Biocondcutor package.
getReactomeCollection	Retrieve gene set collections from from reactome.db
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.

-- H --

hasGeneSet	Check to see if the GeneSetDb has a collection,name GeneSet defined
hasGeneSetCollection	Check if a collection exists in the 'GeneSetDb'

-- I --

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.
is.conformed	(Re)-map geneset IDs to the rows in an expression object.

-- L --

length-method	Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult
logFC	Extract the individual fold changes statistics for elements in the expression object.

-- M --

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)

-- N --

nrow-method

Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult

-- O --

ora	Performs an overrepresentation analysis, (optionally) accounting for bias.

-- P --

p.matrix	Assembles a matrix of nominal or adjusted pvalues from a sparrow::seas result
plot_ora_bias	Performs an overrepresentation analysis, (optionally) accounting for bias.

-- R --

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.
result	Interrogate the results of a sparrow::seas analysis stored in a SparrowResult
result.SparrowResult	Interrogate the results of a sparrow::seas analysis stored in a SparrowResult
resultNames	Interrogate the results of a sparrow::seas analysis stored in a SparrowResult
results	Interrogate the results of a sparrow::seas analysis stored in a SparrowResult

-- S --

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.
SparrowResult	A SparrowResult object holds the results from a sparrow::seas() call.
SparrowResult-class	A SparrowResult object holds the results from a sparrow::seas() call.
sparrow_methods	Lists the supported GSEA methods by sparrow
species_info	Match a species query to the regularized species info.
split_gskey	Converts collection,name combination to key for geneset
ssGSEA.normalize	Normalize a vector of ssGSEA scores in the ssGSEA way.
subset.GeneSetDb	Subset GeneSetDb to only include specified genesets.
subsetByFeatures	Subset a GeneSetDb to only include geneSets with specified features.
subsetByFeatures-method	Subset a GeneSetDb to only include geneSets with specified features.

-- T --

tabulateResults

Interrogate the results of a sparrow::seas analysis stored in a SparrowResult

-- U --

unconform	(Re)-map geneset IDs to the rows in an expression object.
unconform-method	(Re)-map geneset IDs to the rows in an expression object.

-- V --

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

-- Z --

zScore

Calculate single sample geneset score by average z-score method

-- misc --

.GeneSetDb	A container for geneset definitions.
.SparrowResult	A SparrowResult object holds the results from a sparrow::seas() call.
[-method	Subset whole genesets from a GeneSetDb