Man pages for bioFAM/MOFA2
Multi-Omics Factor Analysis v2

add_mofa_factors_to_seuratFunction to add the MOFA representation onto a Seurat object
calculate_contribution_scoresCalculate contribution scores for each view in each sample
calculate_variance_explainedCalculate variance explained by the model
calculate_variance_explained_per_sampleCalculate variance explained by the MOFA factors for each...
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
covariates_namescovariates_names: set and retrieve covariate names
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_covariatesGet sample covariates
get_dataGet data
get_default_data_optionsGet default data options
get_default_mefisto_optionsGet default options for MEFISTO covariates
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_group_kernelGet group covariance matrix
get_imputed_dataGet imputed data
get_interpolated_factorsGet interpolated factor values
get_lengthscalesGet lengthscales
get_scalesGet scales
get_variance_explainedGet variance explained values
get_weightsGet weights
groups_namesgroups_names: set and retrieve group names
imputeImpute missing values from a fitted MOFA
interpolate_factorsInterpolate factors in MEFISTO based on new covariate values
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_alignmentPlot covariate alignment acorss groups
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_data_vs_covScatterplots of feature values against sample covariates
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_factors_vs_covScatterplots of a factor's values againt the sample...
plot_group_kernelHeatmap plot showing the group-group correlations per factor
plot_interpolation_vs_covariatePlot interpolated factors versus covariate (1-dimensional)
plot_sharednessBarplot showing the sharedness per factor
plot_smoothnessBarplot showing the smoothness per factor
plot_top_weightsPlot top weights
plot_variance_explainedPlot variance explained by the model
plot_variance_explained_by_covariatesPlot variance explained by the smooth components of 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...
set_covariatesAdd covariates to a MOFA model
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
bioFAM/MOFA2 documentation built on March 21, 2023, 5:27 p.m.