Package: flashier 1.0.60

flashier: Empirical Bayes Matrix Factorization

Implements empirical Bayes matrix factorization (EBMF), a flexible modeling framework for matrix factorization based on Wang and Stephens (2021) <https://jmlr.org/papers/v22/20-589.html>. Includes many popular matrix factorization methods such as SVD, sparse factor analysis (SFA), non-negative matrix factorization (NMF) and semi-non-negative matrix factorization (semi-NMF) as special cases. The model fitting algorithms are implemented using a modular computational framework that efficiently handles a variety of data types.

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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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
flashier/json (API)

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

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

Datasets:

On CRAN:

Conda:

8.86 score 17 stars 1 packages 586 scripts 435 downloads 46 exports 105 dependencies

Last updated from:fd44811ab2. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK244
source / vignettesOK455
linux-release-x86_64OK222
macos-release-arm64OK152
macos-oldrel-arm64OK151
windows-develOK177
windows-releaseOK179
windows-oldrelOK157
wasm-releaseOK199

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.tabledeconvolveRdigestdplyrdqrngebnmetrunctevaluatefarverfastmapfastTopicsFNNfontawesomefsgenericsggplot2ggrepelgluegtablegtoolshighrhmshtmltoolshtmlwidgetshttrinvgammairlbaisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMatrixmemoisemimemixsqpopensslotelpbapplypillarpkgconfigplotlyplyrPolychromeprettyunitsprogresspromisespurrrquadprogR6rappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppParallelRcppProgressreshape2RhpcBLASctlrlangrmarkdownRSpectraRtsneS7sassscalesscatterplot3dsitmosoftImputeSQUAREMstringistringrsystibbletidyrtidyselecttinytextruncnormtrustutf8uwotvctrsviridisLitewithrxfunyaml

Empirical Bayes non-negative matrix factorization for single-cell RNA-seq data
Preparing the single-cell data for flashier | Variance regularization | Fit a flashier model | Visualizing the cell matrix | Visualizing the gene matrix | Other notes | Session info
Rendered fromflashier_single_cell.Rmdusingknitr::rmarkdown

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

Advanced flashier
Pipeable interface | Customizing the order of operations | An alternative backfitting method | Troubleshooting: turning off extrapolation | Adding an intercept | Fixed sparsity patterns | Modifying the convergence criterion and verbose output | Writing custom convergence criteria and verbose output functions using flash_fit objects | Writing custom EBNM functions | A recipe for plotting fitting progress | Session information
Rendered fromadvanced_flashier.Rmdusingknitr::rmarkdown

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

A closer look at flashier
The EBMF Model | The gtex dataset and the flash() function | Variance structures | Measurement error | Prior families | Backfitting | Sampling from the posterior | Session information
Rendered fromflashier_closer_look.Rmdusingknitr::rmarkdown

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

Introduction to flashier
Session information | Bibliography
Rendered fromflashier_intro.Rmdusingknitr::rmarkdown

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