Massive and Integrative Gene Set Analysis

Documentation for package ‘MIGSA’ version 1.2.0

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MIGSA package

-- A --

as.data.frame,MIGSAres	MIGSAres exploratory functions
as.data.frame-method	MIGSAres exploratory functions
as.Genesets	Creates a GeneSetCollection from a list
as.Genesets-method	Creates a GeneSetCollection from a list

-- B --

bcMigsaRes

A MIGSA results object obtained from breast cancer data

-- C --

colnames,MIGSAres	MIGSAres exploratory functions
colnames-method	MIGSAres exploratory functions

-- D --

dim-method	MIGSAres exploratory functions
downloadEnrichrGeneSets	List and download gene sets from enrichr database
downloadEnrichrGeneSets-method	List and download gene sets from enrichr database

-- E --

enrichrGeneSets	List and download gene sets from enrichr database
enrichrGeneSets-method	List and download gene sets from enrichr database
exprData	Accessors for IGSAinput class
ExprData-class	ExprData S4 class implementation in R
exprData-method	Accessors for IGSAinput class
exprData<-	Accessors for IGSAinput class
exprData<--method	Accessors for IGSAinput class

-- F --

filterByGenes	Get or edit MIGSAres with/by genes that contributed to enrichment
filterByGenes-method	Get or edit MIGSAres with/by genes that contributed to enrichment
FitOptions	FitOptions S4 class implementation in R
fitOptions	Accessors for IGSAinput class
FitOptions-class	FitOptions S4 class implementation in R
fitOptions-method	Accessors for IGSAinput class
FitOptions.data.frame	FitOptions S4 class implementation in R
FitOptions.default	FitOptions S4 class implementation in R
fitOptions<-	Accessors for IGSAinput class
fitOptions<--method	Accessors for IGSAinput class

-- G --

genesBarplot	MIGSAres plots
genesBarplot-method	MIGSAres plots
geneSetBarplot	MIGSAres plots
geneSetBarplot-method	MIGSAres plots
Genesets-enrichr	List and download gene sets from enrichr database
geneSetsFromFile	Creates a GeneSetCollection object from a file
geneSetsFromFile-method	Creates a GeneSetCollection object from a file
geneSetsList	Accessors for IGSAinput class
geneSetsList-method	Accessors for IGSAinput class
geneSetsList<-	Accessors for IGSAinput class
geneSetsList<--method	Accessors for IGSAinput class
genesHeatmap	MIGSAres plots
genesHeatmap-method	MIGSAres plots
genesInSets	Get or edit MIGSAres with/by genes that contributed to enrichment
genesInSets-method	Get or edit MIGSAres with/by genes that contributed to enrichment
getAdditionalInfo	Gets additional information about enrichment results
getAdditionalInfo,MIGSAres	Gets additional information about enrichment results
getAdditionalInfo-method	Gets additional information about enrichment results
getDEGenes	Calculate differentialy expressed genes of an IGSAinput object
getDEGenes,IGSAinput	Calculate differentialy expressed genes of an IGSAinput object
getDEGenes-method	Calculate differentialy expressed genes of an IGSAinput object
getHeights	Explore Gene Ontology gene sets in MIGSAres
getHeights-method	Explore Gene Ontology gene sets in MIGSAres
goTree	Explore Gene Ontology gene sets in MIGSAres
goTree-method	Explore Gene Ontology gene sets in MIGSAres
GSEAparams	GSEAparams S4 class implementation in R
gseaParams	Accessors for IGSAinput class
GSEAparams-class	GSEAparams S4 class implementation in R
gseaParams-method	Accessors for IGSAinput class
gseaParams<-	Accessors for IGSAinput class
gseaParams<--method	Accessors for IGSAinput class

-- H --

head,MIGSAres	MIGSAres exploratory functions
head-method	MIGSAres exploratory functions

-- I --

IGSAinput	IGSAinput S4 class implementation in R
IGSAinput-class	IGSAinput S4 class implementation in R
IGSAinput-getterSetters	Accessors for IGSAinput class

-- L --

loadGo	Creates a GeneSetCollection object using the Gene Ontology data base
loadGo-method	Creates a GeneSetCollection object using the Gene Ontology data base

-- M --

merge,MIGSAres,MIGSAres	MIGSAres exploratory functions
merge-method	MIGSAres exploratory functions
MIGSA	MIGSA execution
MIGSA,list	MIGSA execution
MIGSA-method	MIGSA execution
migsaGoTree	Explore Gene Ontology gene sets in MIGSAres
migsaGoTree-method	Explore Gene Ontology gene sets in MIGSAres
migsaHeatmap	MIGSAres plots
migsaHeatmap-method	MIGSAres plots
MIGSAmGSZ	MIGSAmGSZ
MIGSAmGSZ-method	MIGSAmGSZ
MIGSAPackage	MIGSA package
migsaRes	A MIGSA results object (MIGSAres) example
MIGSAres-class	MIGSAres S4 class implementation in R
MIGSAres-common	MIGSAres exploratory functions
MIGSAres-genes	Get or edit MIGSAres with/by genes that contributed to enrichment
MIGSAres-GOanalysis	Explore Gene Ontology gene sets in MIGSAres
MIGSAres-plots	MIGSAres plots

-- N --

name	Accessors for IGSAinput class
name-method	Accessors for IGSAinput class
name<-	Accessors for IGSAinput class
name<--method	Accessors for IGSAinput class

-- S --

SEAparams	SEAparams S4 class implementation in R
seaParams	Accessors for IGSAinput class
SEAparams-class	SEAparams S4 class implementation in R
seaParams-method	Accessors for IGSAinput class
seaParams<-	Accessors for IGSAinput class
seaParams<--method	Accessors for IGSAinput class
setEnrCutoff	Set enrichment cutoff for a MIGSAres object
setEnrCutoff-method	Set enrichment cutoff for a MIGSAres object
show,MIGSAres	MIGSAres exploratory functions
show-method	MIGSAres exploratory functions
summary	Summary functions for some MIGSA classes
summary-method	Summary functions for some MIGSA classes
summary.GSEAparams	Summary functions for some MIGSA classes
summary.IGSAinput	Summary functions for some MIGSA classes
summary.MIGSAres	Summary functions for some MIGSA classes
summary.SEAparams	Summary functions for some MIGSA classes

-- T --

tail,MIGSAres	MIGSAres exploratory functions
tail-method	MIGSAres exploratory functions

-- misc --

$-method	MIGSAres exploratory functions
[-method	MIGSAres exploratory functions