Package: flashier 1.0.54

flashier: Empirical Bayes Matrix Factorization

Methods for matrix factorization based on Wang and Stephens (2021) <https://jmlr.org/papers/v22/20-589.html>.

Authors:Jason Willwerscheid [aut, cre], Peter Carbonetto [aut], Wei Wang [aut], Matthew Stephens [aut], Eric Weine [ctb], Annie Xie [ctb], Gao Wang [ctb]

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flashier.pdf |flashier.html✨
flashier/json (API)

# Install 'flashier' in R:
install.packages('flashier', repos = c('https://willwerscheid.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/willwerscheid/flashier/issues

Datasets:

On CRAN:

8.29 score 10 stars 224 scripts 247 downloads 46 exports 107 dependencies

Last updated 1 months agofrom:010d3905b3. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-winOKNov 17 2024
R-4.5-linuxOKNov 17 2024
R-4.4-winOKNov 17 2024
R-4.4-macOKNov 17 2024
R-4.3-winOKNov 17 2024
R-4.3-macOKNov 17 2024

Exports:flashflash_add_interceptflash_backfitflash_clear_timeoutflash_conv_crit_elbo_diffflash_conv_crit_max_chgflash_conv_crit_max_chg_Fflash_conv_crit_max_chg_Lflash_ebnmflash_factors_fixflash_factors_initflash_factors_removeflash_factors_reorderflash_factors_set_to_zeroflash_factors_unfixflash_fitflash_fit_get_elboflash_fit_get_est_tauflash_fit_get_fixed_tauflash_fit_get_gflash_fit_get_KLflash_fit_get_p2mflash_fit_get_pmflash_fit_get_tauflash_greedyflash_greedy_init_defaultflash_greedy_init_irlbaflash_greedy_init_softImputeflash_initflash_nullcheckflash_plot_barflash_plot_heatmapflash_plot_histogramflash_plot_scatterflash_plot_screeflash_plot_structureflash_set_conv_critflash_set_timeoutflash_set_verboseflash_update_dataflash_verbose_elboflash_verbose_elbo_diffflash_verbose_max_chgflash_verbose_max_chg_Fflash_verbose_max_chg_Lldf

Dependencies:ashraskpassbase64encBHbslibcachemclicolorspacecowplotcpp11crayoncrosstalkcurldata.tabledeconvolveRdigestdplyrdqrngebnmetrunctevaluatefansifarverfastmapfastTopicsFNNfontawesomefsgenericsggplot2ggrepelgluegtablegtoolshighrhmshorseshoehtmltoolshtmlwidgetshttrinvgammairlbaisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemixsqpmunsellnlmeopensslpbapplypillarpkgconfigplotlyPolychromeprettyunitsprogresspromisespurrrquadprogR6rappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppParallelRcppProgressRhpcBLASctlrlangrmarkdownRSpectraRtsnesassscalesscatterplot3dsitmosoftImputeSQUAREMstringistringrsystibbletidyrtidyselecttinytextruncnormtrustutf8uwotvctrsviridisLitewithrxfunyaml

A closer look at flashier

Rendered fromflashier_closer_look.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-04-30
Started: 2024-02-21

Advanced flashier

Rendered fromadvanced_flashier.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-04-30
Started: 2024-02-21

Empirical Bayes non-negative matrix factorization for single-cell RNA-seq data

Rendered fromflashier_single_cell.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-05-06
Started: 2024-04-03

Introduction to flashier

Rendered fromflashier_intro.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-04-30
Started: 2024-02-21

Readme and manuals

Help Manual

Help pageTopics
Fitted method for flash objectsfitted.flash
Fitted method for flash fit objectsfitted.flash_fit
Empirical Bayes matrix factorizationflash
Add "intercept" to a flash objectflash_add_intercept
Backfit a flash objectflash_backfit
Set timeoutflash_clear_timeout
Calculate the difference in ELBOflash_conv_crit_elbo_diff
Calculate the maximum absolute difference in scaled loadings and factorsflash_conv_crit_max_chg
Calculate the maximum absolute difference in scaled factorsflash_conv_crit_max_chg_F
Calculate the maximum absolute difference in scaled loadingsflash_conv_crit_max_chg_L
Construct an EBNM functionflash_ebnm
Fix flash factorsflash_factors_fix
Initialize flash factors at specified valuesflash_factors_init
Remove factors from a flash objectflash_factors_remove
Reorder factors in a flash objectflash_factors_reorder
Set flash factors to zeroflash_factors_set_to_zero
Unfix flash factorsflash_factors_unfix
Extract a flash_fit objectflash_fit flash_fit_get_elbo flash_fit_get_est_tau flash_fit_get_fixed_tau flash_fit_get_g flash_fit_get_KL flash_fit_get_p2m flash_fit_get_pm flash_fit_get_tau
Greedily add factors to a flash objectflash_greedy
Initialize a flash factorflash_greedy_init_default
Initialize a flash factor using IRLBAflash_greedy_init_irlba
Initialize a flash factor using softImputeflash_greedy_init_softImpute
Initialize flash objectflash_init
Nullcheck flash factorsflash_nullcheck
Create bar plots of factors or loadings for a flash fitflash_plot_bar
Create heatmap of factors or loadings for a flash fitflash_plot_heatmap
Create histograms of factors or loadings for a flash fitflash_plot_histogram
Create scatter plots of factors or loadings for a flash fitflash_plot_scatter
Create a scree plot for a flash fitflash_plot_scree
Create structure plot of factors or loadings for a flash fitflash_plot_structure
Set convergence criterion and tolerance parameterflash_set_conv_crit
Set timeoutflash_set_timeout
Set verbose outputflash_set_verbose
Update data in a flash objectflash_update_data
Display the current ELBOflash_verbose_elbo
Display the difference in ELBOflash_verbose_elbo_diff
Display the maximum difference in scaled loadings and factorsflash_verbose_max_chg
Display the maximum difference in scaled factorsflash_verbose_max_chg_F
Display the maximum difference in scaled loadingsflash_verbose_max_chg_L
GTEx datagtex
Colors for plotting GTEx datagtex_colors
LDF method for flash and flash fit objectsldf ldf.flash ldf.flash_fit
Plot method for flash objectsplot.flash
Residuals method for flash objectsresiduals.flash
Residuals method for flash fit objectsresiduals.flash_fit