# Massive and Integrative Gene Set Analysis

## Documentation for package ‘MIGSA’ version 1.12.0

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

## Help Pages

A B C D E F G H I L M N S T misc

## -- 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