# Multi-Omics Factor Analysis (MOFA)

## Documentation for package ‘MOFA’ version 1.0.0

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

## Help Pages

C D E F G I L M P Q R S T V

MOFA-package | Multi-Omics Factor Analysis (MOFA)

## -- C --

calculateVarianceExplained | Calculate variance explained by the model
clusterSamples | clusterSamples: K-means clustering on samples based on latent factors
compareFactors | Correlation of the latent factors across different trials
compareModels | Compare different instances of trained 'MOFAmodel'
createMOFAobject | Initialize a MOFA object

## -- D --

DataOptions | DataOptions: set and retrieve data options
DataOptions-method | DataOptions: set and retrieve data options
DataOptions<- | DataOptions: set and retrieve data options
DataOptions<--method | DataOptions: set and retrieve data options
Dimensions | Dimensions: set and retrieve dimensions
Dimensions-method | Dimensions: set and retrieve dimensions
Dimensions<- | Dimensions: set and retrieve dimensions
Dimensions<--method | Dimensions: set and retrieve dimensions

## -- E --

Expectations | Expectations: set and retrieve expectations of model components
Expectations-method | Expectations: set and retrieve expectations of model components
Expectations<- | Expectations: set and retrieve expectations of model components
Expectations<--method | Expectations: set and retrieve expectations of model components

## -- F --

factorNames | factorNames: set and retrieve factor names
factorNames-method | factorNames: set and retrieve factor names
factorNames<- | factorNames: set and retrieve factor names
factorNames<--method | factorNames: set and retrieve factor names
FeatureIntercepts | FeatureIntercepts: set and retrieve feature intercepts
FeatureIntercepts-method | FeatureIntercepts: set and retrieve feature intercepts
FeatureIntercepts<- | FeatureIntercepts: set and retrieve feature intercepts
FeatureIntercepts<--method | FeatureIntercepts: set and retrieve feature intercepts
featureNames | featureNames: set and retrieve feature names
featureNames-method | featureNames: set and retrieve feature names
featureNames<- | featureNames: set and retrieve feature names
featureNames<--method | featureNames: set and retrieve feature names

## -- G --

getCovariates | getCovariates
getDefaultDataOptions | Get default data options
getDefaultModelOptions | Get default model options
getDefaultTrainOptions | Get default training options
getDimensions | getDimensions
getELBO | getELBO
getExpectations | getExpectations
getFactors | getFactors
getImputedData | getImputedData
getTrainData | getTrainData
getWeights | getWeights

## -- I --

impute | Impute missing values from a fitted MOFA model
ImputedData | ImputedData: set and retrieve imputed data
ImputedData-method | ImputedData: set and retrieve imputed data
ImputedData<- | ImputedData: set and retrieve imputed data
ImputedData<--method | ImputedData: set and retrieve imputed data
InputData | InputData: set and retrieve input data
InputData-method | InputData: set and retrieve input data
InputData<- | InputData: set and retrieve input data
InputData<--method | InputData: set and retrieve input data

## -- L --

loadModel | loading a trained MOFA model

## -- M --

makeExampleData | make an example multi-view data set for illustration of MOFA
ModelOptions | ModelOptions: set and retrieve model options
ModelOptions-method | ModelOptions: set and retrieve model options
ModelOptions<- | ModelOptions: set and retrieve model options
ModelOptions<--method | ModelOptions: set and retrieve model options
MOFA | Multi-Omics Factor Analysis (MOFA)
MOFAmodel | Class to store a Multi-Omics Factor Analysis (MOFA) model
MOFAmodel-class | Class to store a Multi-Omics Factor Analysis (MOFA) model

## -- P --

plotDataHeatmap | Plot heatmap of relevant features
plotDataOverview | Plot overview of the input data
plotDataScatter | Scatterplots of feature values against latent factors
plotEnrichment | Plot output of Feature Set Enrichment Analysis
plotEnrichmentBars | Barplot of Feature Set Enrichment Analysis results
plotEnrichmentDetailed | Plot detailed output of the Feature Set Enrichment Analysis
plotEnrichmentHeatmap | Heatmap of Feature Set Enrichment Analysis results
plotFactorBeeswarm | Beeswarm plot of latent factors
plotFactorCor | Plot correlation matrix between latent factors
plotFactorHist | Plot histogram of latent factor values
plotFactorScatter | Scatterplot of two latent factors
plotFactorScatters | Pairwise scatterplots of multiple latent factors
plotTopWeights | Plot top weights
plotVarianceExplained | Plot variance explained by the model
plotWeights | Plot Weights
plotWeightsHeatmap | Plot heatmap of the weights
predict | Do predictions using a fitted MOFA model
prepareMOFA | prepare a MOFAobject for training

## -- Q --

qualityControl | qualityControl

## -- R --

regressCovariates | regress out a covariate from the training data
runEnrichmentAnalysis | Feature Set Enrichment Analysis
runMOFA | train a MOFA model

## -- S --

sampleNames | sampleNames: set and retrieve sample names
sampleNames-method | sampleNames: set and retrieve sample names
sampleNames<- | sampleNames: set and retrieve sample names
sampleNames<--method | sampleNames: set and retrieve sample names
selectModel | Select the best model from a list of trained 'MOFAmodel' objects
Status | Status: set and retrieve training status
Status-method | Status: set and retrieve training status
Status<- | Status: set and retrieve training status
Status<--method | Status: set and retrieve training status
subsetFactors | Subset factors
subsetSamples | Subset samples
subsetViews | Subset views

## -- T --

trainCurveELBO | Training curve for Evidence Lower Bound (ELBO)
trainCurveFactors | Training curve for the number of active factors
TrainData | TrainData: set and retrieve training data
TrainData-method | TrainData: set and retrieve training data
TrainData<- | TrainData: set and retrieve training data
TrainData<--method | TrainData: set and retrieve training data
TrainOptions | TrainOptions: set and retrieve training options
TrainOptions-method | TrainOptions: set and retrieve training options
TrainOptions<- | TrainOptions: set and retrieve training options
TrainOptions<--method | TrainOptions: set and retrieve training options
TrainStats | TrainStats: set and retrieve training statistcs
TrainStats-method | TrainStats: set and retrieve training statistcs
TrainStats<- | TrainStats: set and retrieve training statistcs
TrainStats<--method | TrainStats: set and retrieve training statistcs

## -- V --

viewNames | viewNames: set and retrieve view names
viewNames-method | viewNames: set and retrieve view names
viewNames<- | viewNames: set and retrieve view names
viewNames<--method | viewNames: set and retrieve view names