API for bioFAM/MOFA
Multi-Omics Factor Analysis (MOFA)

Global functions
.computefeatureStatistics	Source code
.createMAEobjectFromList	Source code
.createMOFAobjectFromMAE	Source code
.createVarGroupList	Source code
.detectInterceptFactors	Source code
.detectPassengers	Source code
.inferLikelihoods	Source code
.pcgse	Source code
.pcgseViaTTest	Source code
.pcgseViaWMW	Source code
.setNames	Source code
.subset_augment	Source code
.updateOldModel	Source code
DataOptions	Man page
DataOptions,MOFAmodel-method	Man page
DataOptions<-	Man page
DataOptions<-,MOFAmodel,list-method	Man page
Dimensions	Man page
Dimensions,MOFAmodel-method	Man page
Dimensions<-	Man page
Dimensions<-,MOFAmodel,list-method	Man page
Expectations	Man page
Expectations,MOFAmodel-method	Man page
Expectations<-	Man page
Expectations<-,MOFAmodel,list-method	Man page
FeatureIntercepts	Man page
FeatureIntercepts,MOFAmodel-method	Man page
FeatureIntercepts<-	Man page
FeatureIntercepts<-,MOFAmodel,list-method	Man page
ImputedData	Man page
ImputedData,MOFAmodel-method	Man page
ImputedData<-	Man page
ImputedData<-,MOFAmodel,list-method	Man page
InputData	Man page
InputData,MOFAmodel-method	Man page
InputData<-	Man page
InputData<-,MOFAmodel,MultiAssayExperiment-method	Man page
MOFA	Man page
MOFA-package	Man page
MOFAmodel	Man page
MOFAmodel-class	Man page
ModelOptions	Man page
ModelOptions,MOFAmodel-method	Man page
ModelOptions<-	Man page
ModelOptions<-,MOFAmodel,list-method	Man page
Status	Man page
Status,MOFAmodel-method	Man page
Status<-	Man page
Status<-,MOFAmodel,character-method	Man page
TrainData	Man page
TrainData,MOFAmodel-method	Man page
TrainData<-	Man page
TrainData<-,MOFAmodel,list-method	Man page
TrainOptions	Man page
TrainOptions,MOFAmodel-method	Man page
TrainOptions<-	Man page
TrainOptions<-,MOFAmodel,list-method	Man page
TrainStats	Man page
TrainStats,MOFAmodel-method	Man page
TrainStats<-	Man page
TrainStats<-,MOFAmodel,list-method	Man page
calculateVarianceExplained	Man page Source code
clusterSamples	Man page Source code
compareFactors	Man page Source code
compareModels	Man page Source code
createMOFAobject	Man page Source code
factorNames	Man page
factorNames,MOFAmodel-method	Man page
factorNames<-	Man page
factorNames<-,MOFAmodel,vector-method	Man page
featureNames	Man page
featureNames,MOFAmodel-method	Man page
featureNames<-	Man page
featureNames<-,MOFAmodel,list-method	Man page
flip_factor	Source code
getCovariates	Man page Source code
getDefaultDataOptions	Man page Source code
getDefaultModelOptions	Man page Source code
getDefaultTrainOptions	Man page Source code
getDimensions	Man page Source code
getELBO	Man page Source code
getExpectations	Man page Source code
getFactors	Man page Source code
getImputedData	Man page Source code
getTrainData	Man page Source code
getWeights	Man page Source code
impute	Man page Source code
loadModel	Man page Source code
makeExampleData	Man page Source code
plotDataHeatmap	Man page Source code
plotDataOverview	Man page Source code
plotDataScatter	Man page Source code
plotEnrichment	Man page Source code
plotEnrichmentBars	Man page Source code
plotEnrichmentDetailed	Man page Source code
plotEnrichmentHeatmap	Man page Source code
plotFactorBeeswarm	Man page Source code
plotFactorCor	Man page Source code
plotFactorHist	Man page Source code
plotFactorScatter	Man page
plotFactorScatters	Man page Source code
plotTopWeights	Man page Source code
plotVarianceExplained	Man page Source code
plotWeights	Man page Source code
plotWeightsHeatmap	Man page Source code
predict	Man page Source code
prepareMOFA	Man page Source code
qualityControl	Man page Source code
regressCovariates	Man page Source code
runEnrichmentAnalysis	Man page Source code
runMOFA	Man page Source code
sampleNames	Man page
sampleNames,MOFAmodel-method	Man page
sampleNames<-	Man page
sampleNames<-,MOFAmodel,vector-method	Man page
selectModel	Man page Source code
subsetFactors	Man page Source code
subsetSamples	Man page Source code
subsetViews	Man page Source code
subset_augment	Source code
trainCurveELBO	Man page Source code
trainCurveFactors	Man page Source code
viewNames	Man page
viewNames,MOFAmodel-method	Man page
viewNames<-	Man page
viewNames<-,MOFAmodel,character-method	Man page