Massive and Integrative Gene Set Analysis

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Documentation for package ‘MIGSA’ version 1.16.0

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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