Multi-Omics Factor Analysis (MOFA)


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Documentation for package ‘MOFA’ version 1.6.1

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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