A B C D E F G H I L M N S T misc
MIGSAPackage-package | MIGSA package |
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 |
bcMigsaRes | A MIGSA results object obtained from breast cancer data |
colnames,MIGSAres | MIGSAres exploratory functions |
colnames-method | MIGSAres exploratory functions |
dim-method | MIGSAres exploratory functions |
downloadEnrichrGeneSets | List and download gene sets from enrichr database |
downloadEnrichrGeneSets-method | List and download gene sets from enrichr database |
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 |
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 |
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 |
head,MIGSAres | MIGSAres exploratory functions |
head-method | MIGSAres exploratory functions |
IGSAinput | IGSAinput S4 class implementation in R |
IGSAinput-class | IGSAinput S4 class implementation in R |
IGSAinput-getterSetters | Accessors for IGSAinput class |
loadGo | Creates a GeneSetCollection object using the Gene Ontology data base |
loadGo-method | Creates a GeneSetCollection object using the Gene Ontology data base |
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 |
name | Accessors for IGSAinput class |
name-method | Accessors for IGSAinput class |
name<- | Accessors for IGSAinput class |
name<--method | Accessors for IGSAinput class |
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 |
tail,MIGSAres | MIGSAres exploratory functions |
tail-method | MIGSAres exploratory functions |
$-method | MIGSAres exploratory functions |
[-method | MIGSAres exploratory functions |