Empirical Bayes Matrix Factorization
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Documentation for package ‘flashier’ version 1.0.7
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 |