# Empirical Bayes Matrix Factorization

## Documentation for package ‘flashier’ version 1.0.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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 | Extract a flash_fit object
flash_fit_get_elbo | Extract a flash_fit object
flash_fit_get_est_tau | Extract a flash_fit object
flash_fit_get_fixed_tau | Extract a flash_fit object
flash_fit_get_g | Extract a flash_fit object
flash_fit_get_KL | Extract a flash_fit object
flash_fit_get_p2m | Extract a flash_fit object
flash_fit_get_pm | Extract a flash_fit object
flash_fit_get_tau | 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_set_conv_crit | Set convergence criterion and tolerance parameter
flash_set_timeout | Set timeout
flash_set_verbose | Set verbose output
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
ldf.flash | LDF method for flash and flash fit objects
ldf.flash_fit | 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