Function reference • MOFAcellulaR

All functions

center_views(): Center view-data

create_init_exp(): Single-cell SummarizedExperiment object

filt_gex_bybckgrnd(): Filter background expression of marker genes

filt_gex_byexpr(): Filter lowly expressed genes from pseudobulk profiles

filt_gex_byhvg(): Indentify highly variable genes

filt_profiles(): Filter pseudobulk profiles

filt_samples_bycov(): Filter samples that have a limited coverage of features in a view

filt_views_bygenes(): Filter views with not enough features

filt_views_bysamples(): Filter views with not enough samples

get_associations(): Associate factors to covariates of interest

get_geneweights(): Extract feature weights scores from a model in a tidy format for a factor of interest

get_tidy_factors(): Extract factor scores from a model in a tidy format with meta data

pb_dat2MOFA(): Create MOFA-ready dataframe

plot_MOFA_hmap(): Visualize MOFA multicellular model

plot_sample_2D(): Visualize sample variability in a 2D space

project_data(): Project new data into a known factor space

tmm_trns(): TMM normalization of single cell data sets