Man pages for MOFA2
Multi-Omics Factor Analysis v2

calculate_variance_explainedCalculate variance explained by the model
cluster_samplesK-means clustering on samples based on latent factors
compare_elboCompare different trained 'MOFA' objects in terms of the...
compare_factorsPlot the correlation of factors between different models
correlate_factors_with_covariatesPlot correlation of factors with external covariates
create_mofacreate a MOFA object
create_mofa_from_dfcreate a MOFA object from a data.frame object
create_mofa_from_matrixcreate a MOFA object from a a list of matrices
create_mofa_from_MultiAssayExperimentcreate a MOFA object from a MultiAssayExperiment object
create_mofa_from_Seuratcreate a MOFA object from a Seurat object
create_mofa_from_SingleCellExperimentcreate a MOFA object from a SingleCellExperiment object
factors_namesfactors_names: set and retrieve factor names
features_metadatafeatures_metadata: set and retrieve feature metadata
features_namesfeatures_names: set and retrieve feature names
get_dataGet data
get_default_data_optionsGet default data options
get_default_model_optionsGet default model options
get_default_stochastic_optionsGet default stochastic options
get_default_training_optionsGet default training options
get_dimensionsGet dimensions
get_elboGet ELBO
get_expectationsGet expectations
get_factorsGet factors
get_imputed_dataGet imputed data
get_variance_explainedGet variance explained values
get_weightsGet weights
groups_namesgroups_names: set and retrieve group names
imputeImpute missing values from a fitted MOFA
load_modelLoad a trained MOFA
make_example_dataSimulate a data set using the generative model of MOFA
MOFAClass to store a mofa model
pipeRe-exporting the pipe operator See 'magrittr::%>%' for...
plot_ascii_dataVisualize the structure of the data in the terminal
plot_data_heatmapPlot heatmap of relevant features
plot_data_overviewOverview of the input data
plot_data_scatterScatterplots of feature values against latent factors
plot_dimredPlot dimensionality reduction based on MOFA factors
plot_enrichmentPlot output of gene set Enrichment Analysis
plot_enrichment_detailedPlot detailed output of the Feature Set Enrichment Analysis
plot_enrichment_heatmapHeatmap of Feature Set Enrichment Analysis results
plot_factorBeeswarm plot of factor values
plot_factor_corPlot correlation matrix between latent factors
plot_factorsScatterplots of two factor values
plot_top_weightsPlot top weights
plot_variance_explainedPlot variance explained by the model
plot_variance_explained_per_featurePlot variance explained by the model for a set of features...
plot_weightsPlot distribution of feature weights (weights)
plot_weights_heatmapPlot heatmap of the weights
plot_weights_scatterScatterplots of weights
predictDo predictions using a fitted MOFA
prepare_mofaPrepare a MOFA for training
run_enrichmentRun feature set Enrichment Analysis
run_mofaTrain a MOFA model
run_tsneRun t-SNE on the MOFA factors
run_umapRun UMAP on the MOFA factors
samples_metadatasamples_metadata: retrieve sample metadata
samples_namessamples_names: set and retrieve sample names
select_modelSelect a model from a list of trained 'MOFA' objects based on...
subset_factorsSubset factors
subset_featuresSubset features
subset_groupsSubset groups
subset_samplesSubset samples
subset_viewsSubset views
summarise_factorsSummarise factor values using external groups
views_namesviews_names: set and retrieve view names
MOFA2 documentation built on Nov. 8, 2020, 7:28 p.m.