bioFAM/MOFA2
Multi-Omics Factor Analysis v2

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33
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bioFAM/MOFA2: Multi-Omics Factor Analysis v2
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API

API for bioFAM/MOFA2
Multi-Omics Factor Analysis v2

Global functions
%>% Man page
.add_column_to_metadata Source code
.add_legend Source code
.check_and_get_covariates Source code
.check_and_get_factors Source code
.check_and_get_features_from_view Source code
.check_and_get_groups Source code
.check_and_get_samples Source code
.check_and_get_views Source code
.compute_feature_statistics Source code
.cpaste Source code
.createVarGroupList Source code
.create_features_metadata Source code
.create_matrix_placeholder Source code
.create_samples_metadata Source code
.detect_outliers Source code
.df_to_matrix Source code
.flip_factor Source code
.get_nodes_types Source code
.get_top_features_by_loading Source code
.infer_likelihoods Source code
.insert_inside Source code
.name_views_and_groups Source code
.pad_left Source code
.pad_left_with Source code
.pcgse Source code
.pcgse_ttest Source code
.pcgse_wmw Source code
.plot_factors_vs_cov_1d Source code
.plot_factors_vs_cov_2d Source code
.plot_multiple_factors Source code
.quality_control Source code
.rename_duplicated_features Source code
.rep_string Source code
.run_mofa_reticulate Source code
.select_axis.text.size Source code
.select_pearson_text_size Source code
.select_stroke Source code
.set_colorby Source code
.set_colorby_features Source code
.set_data_names Source code
.set_expectations_names Source code
.set_groupby Source code
.set_imputed_data_names Source code
.set_shapeby Source code
.set_shapeby_features Source code
.set_xax Source code
.split_data_into_groups Source code
.split_sce_into_groups Source code
.split_seurat_into_groups Source code
.subset_augment Source code
MOFA Man page
MOFA-class Man page
add_mofa_factors_to_seurat Man page Source code
calculate_contribution_scores Man page Source code
calculate_variance_explained Man page Source code
calculate_variance_explained_per_sample Man page Source code
cluster_samples Man page Source code
compare_elbo Man page Source code
compare_factors Man page Source code
correlate_factors_with_covariates Man page Source code
covariates,MOFA-method Man page
covariates_names Man page
covariates_names,MOFA-method Man page
covariates_names<- Man page
covariates_names<-,MOFA,vector-method Man page
create_mofa Man page Source code
create_mofa_from_MultiAssayExperiment Man page Source code
create_mofa_from_Seurat Man page Source code
create_mofa_from_SingleCellExperiment Man page Source code
create_mofa_from_df Man page Source code
create_mofa_from_matrix Man page Source code
factors_names Man page
factors_names,MOFA-method Man page
factors_names<- Man page
factors_names<-,MOFA,vector-method Man page
features_metadata Man page
features_metadata,MOFA-method Man page
features_metadata<- Man page
features_metadata<-,MOFA,data.frame-method Man page
features_names Man page
features_names,MOFA-method Man page
features_names<- Man page
features_names<-,MOFA,list-method Man page
get_contribution_scores Source code
get_covariates Man page Source code
get_data Man page Source code
get_default_data_options Man page Source code
get_default_mefisto_options Man page Source code
get_default_model_options Man page Source code
get_default_stochastic_options Man page Source code
get_default_training_options Man page Source code
get_dimensions Man page Source code
get_elbo Man page Source code
get_expectations Man page Source code
get_factors Man page Source code
get_group_kernel Man page Source code
get_imputed_data Man page Source code
get_interpolated_factors Man page Source code
get_lengthscales Man page Source code
get_scales Man page Source code
get_variance_explained Man page Source code
get_weights Man page Source code
groups_names Man page
groups_names,MOFA-method Man page
groups_names<- Man page
groups_names<-,MOFA,character-method Man page
impute Man page Source code
interpolate_factors Man page Source code
load_model Man page Source code
make_example_data Man page Source code
plot_alignment Man page
plot_ascii_data Man page Source code
plot_contribution_scores Source code
plot_data_heatmap Man page Source code
plot_data_overview Man page Source code
plot_data_scatter Man page Source code
plot_data_vs_cov Man page Source code
plot_dimred Man page Source code
plot_enrichment Man page Source code
plot_enrichment_detailed Man page Source code
plot_enrichment_heatmap Man page Source code
plot_factor Man page Source code
plot_factor_cor Man page Source code
plot_factors Man page Source code
plot_factors_vs_cov Man page Source code
plot_group_kernel Man page Source code
plot_interpolation_vs_covariate Man page Source code
plot_sharedness Man page Source code
plot_smoothness Man page Source code
plot_top_weights Man page Source code
plot_variance_explained Man page Source code
plot_variance_explained_by_covariates Man page
plot_variance_explained_per_feature Man page Source code
plot_weights Man page Source code
plot_weights_heatmap Man page Source code
plot_weights_scatter Man page
predict Man page Source code
prepare_mofa Man page Source code
run_enrichment Man page Source code
run_mofa Man page Source code
run_tsne Man page Source code
run_umap Man page Source code
samples_metadata Man page
samples_metadata,MOFA-method Man page
samples_metadata<- Man page
samples_metadata<-,MOFA,data.frame-method Man page
samples_names Man page
samples_names,MOFA-method Man page
samples_names<- Man page
samples_names<-,MOFA,list-method Man page
select_model Man page Source code
set_covariates Man page Source code
subset_factors Man page Source code
subset_features Man page Source code
subset_groups Man page Source code
subset_samples Man page Source code
subset_views Man page Source code
summarise_factors Man page Source code
views_names Man page
views_names,MOFA-method Man page
views_names<- Man page
views_names<-,MOFA,character-method Man page
bioFAM/MOFA2 documentation built on June 12, 2024, 3:57 p.m.

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