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
bioFAM/MOFA documentation built on Nov. 7, 2019, 11:01 p.m.