# Take command of set enrichment analyses through a unified interface

## Documentation for package ‘sparrow’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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