Function reference • flashier

All functions
`fitted(<flash>)`	Fitted method for flash objects
`fitted(<flash_fit>)`	Fitted method for flash fit objects
`flash()`	Empirical Bayes matrix factorization
`flash_add_intercept()`	Add "intercept" to a flash object
`flash_backfit()`	Backfit a flash object
`flash_clear_timeout()`	Set timeout
`flash_conv_crit_elbo_diff()`	Calculate the difference in ELBO
`flash_conv_crit_max_chg()`	Calculate the maximum absolute difference in scaled loadings and factors
`flash_conv_crit_max_chg_F()`	Calculate the maximum absolute difference in scaled factors
`flash_conv_crit_max_chg_L()`	Calculate the maximum absolute difference in scaled loadings
`flash_ebnm()`	Construct an EBNM function
`flash_factors_fix()`	Fix flash factors
`flash_factors_init()`	Initialize flash factors at specified values
`flash_factors_remove()`	Remove factors from a flash object
`flash_factors_reorder()`	Reorder factors in a flash object
`flash_factors_set_to_zero()`	Set flash factors to zero
`flash_factors_unfix()`	Unfix flash factors
`flash_fit()` `flash_fit_get_pm()` `flash_fit_get_p2m()` `flash_fit_get_est_tau()` `flash_fit_get_fixed_tau()` `flash_fit_get_tau()` `flash_fit_get_elbo()` `flash_fit_get_KL()` `flash_fit_get_g()`	Extract a flash_fit object
`flash_greedy()`	Greedily add factors to a flash object
`flash_greedy_init_default()`	Initialize a flash factor
`flash_greedy_init_irlba()`	Initialize a flash factor using IRLBA
`flash_greedy_init_softImpute()`	Initialize a flash factor using softImpute
`flash_init()`	Initialize flash object
`flash_nullcheck()`	Nullcheck flash factors
`flash_plot_bar()`	Create bar plots of factors or loadings for a flash fit
`flash_plot_heatmap()`	Create heatmap of factors or loadings for a flash fit
`flash_plot_histogram()`	Create histograms of factors or loadings for a flash fit
`flash_plot_scatter()`	Create scatter plots of factors or loadings for a flash fit
`flash_plot_scree()`	Create a scree plot for a flash fit
`flash_plot_structure()`	Create structure plot of factors or loadings for a flash fit
`flash_set_conv_crit()`	Set convergence criterion and tolerance parameter
`flash_set_timeout()`	Set timeout
`flash_set_verbose()`	Set verbose output
`flash_update_data()`	Update data in a flash object
`flash_verbose_elbo()`	Display the current ELBO
`flash_verbose_elbo_diff()`	Display the difference in ELBO
`flash_verbose_max_chg()`	Display the maximum difference in scaled loadings and factors
`flash_verbose_max_chg_F()`	Display the maximum difference in scaled factors
`flash_verbose_max_chg_L()`	Display the maximum difference in scaled loadings
`gtex`	GTEx data
`gtex_colors`	Colors for plotting GTEx data
`ldf()`	LDF method for flash and flash fit objects
`plot(<flash>)`	Plot method for flash objects
`residuals(<flash>)`	Residuals method for flash objects
`residuals(<flash_fit>)`	Residuals method for flash fit objects

Reference

All functions