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flashier

Functions documentation and vignettes are available here.

Please note that function names changed in Version 0.2.44. If you are using flashier code from previous versions, please make the following substitutions, and note that many parameter names have changed as well:

Old NameNew Name
as.ebnm.fnflash_ebnm
conv.crit.elboflash_conv_crit_elbo_diff
conv.crit.factorsflash_conv_crit_max_chg_F
conv.crit.loadingsflash_conv_crit_max_chg_L
display.elboflash_verbose_elbo
display.elbo.diffflash_verbose_elbo_diff
display.F.max.chgflash_verbose_max_chg_F
display.L.max.chgflash_verbose_max_chg_L
display.max.chgflash_verbose_max_chg
ff.elboflash_fit_get_elbo
ff.est.tauflash_fit_get_est_tau
ff.fixed.tauflash_fit_get_fixed_tau
ff.gflash_fit_get_g
ff.KLflash_fit_get_KL
ff.p2mflash_fit_get_p2m
ff.pmflash_fit_get_pm
ff.tauflash_fit_get_tau
flash.add.greedyflash_greedy
flash.backfitflash_backfit
flash.fitflash_fit
flash.fix.factorsflash_factors_fix
flash.initflash_init
flash.init.factorsflash_factors_init
flash.nullcheckflash_nullcheck
flash.remove.factorsflash_factors_remove
flash.reorder.factorsflash_factors_reorder
flash.set.factors.to.zeroflash_factors_set_to_zero
flash.set.verboseflash_set_verbose
init.fn.defaultflash_greedy_init_default
init.fn.irlbaflash_greedy_init_irlba
init.fn.softImputeflash_greedy_init_softImpute

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Version

Install

install.packages('flashier')

Monthly Downloads

226

Version

1.0.7

License

BSD_3_clause + file LICENSE

Issues

31

Pull Requests

1

Stars

12

Forks

12

Maintainer

Jason Willwerscheid

Last Published

October 17th, 2023

Functions in flashier (1.0.7)

flash_factors_set_to_zero

Set flash factors to zero
flash_ebnm

Construct an EBNM function
flash_factors_reorder

Reorder factors in a flash object
flash_factors_fix

Fix flash factors
flash_factors_remove

Remove factors from a flash object
flash_factors_init

Initialize flash factors at specified values
flash_greedy_init_default

Initialize a flash factor
flash_greedy

Greedily add factors to a flash object
flash_add_intercept

Add "intercept" to a flash object
flash_factors_unfix

Unfix flash factors
flash_fit

Extract a flash_fit object
flash_greedy_init_irlba

Initialize a flash factor using IRLBA
flash_set_conv_crit

Set convergence criterion and tolerance parameter
flash_verbose_elbo_diff

Display the difference in ELBO
flash_verbose_max_chg

Display the maximum difference in scaled loadings and factors
flash_verbose_elbo

Display the current ELBO
flash_set_verbose

Set verbose output
flash_nullcheck

Nullcheck flash factors
flash_init

Initialize flash object
gtex_colors

Colors for plotting GTEx data
flash_set_timeout

Set timeout
gtex

GTEx data
ldf

LDF method for flash and flash fit objects
plot.flash

Plot method for flash objects
flash_verbose_max_chg_F

Display the maximum difference in scaled factors
flash_greedy_init_softImpute

Initialize a flash factor using softImpute
residuals.flash_fit

Residuals method for flash fit objects
residuals.flash

Residuals method for flash objects
flash_verbose_max_chg_L

Display the maximum difference in scaled loadings
flash_backfit

Backfit a flash object
flash_conv_crit_elbo_diff

Calculate the difference in ELBO
fitted.flash

Fitted method for flash objects
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_clear_timeout

Set timeout
flash

Empirical Bayes matrix factorization
flash_conv_crit_max_chg_L

Calculate the maximum absolute difference in scaled loadings
fitted.flash_fit

Fitted method for flash fit objects