Man pages for stephenslab/susieR
Fit Sum of Single Effects Linear Regression Model

check_projectionCheck whether b in space spanned by the non-zero eigenvectors...
check_semi_pdCheck whether A is positive semidefinite
coef.susieextract regression coefficients from susie fit
compute_colSdscomputes column standard deviations for any type of matrix...
compute_MXtComputes M%*%t(standardized.X) using sparse multiplication...
compute_ssCompute the needed summary statistics for 'susie_ss' from the...
compute_tf_cmCompute column mean of the trend filtering matrix X
compute_tf_csdCompute column standard deviation of the trend filtering...
compute_tf_dCompute colSums(X * X) for X under four scenarios
compute_tf_std_dA fast way to compute colSums(X * X), where X is a...
compute_tf_XbCompute unscaled X %*% b using the special structure of trend...
compute_tf_XtyCompute unscaled t(X) %*% y using the special structure of...
compute_XbComputes standardized.X %*% b using sparse multiplication...
compute_XtyComputes t(standardized.X)%*%y using sparse multiplication...
estimate_mad_residual_varianceestimate residual variance using MAD estimator
estimate_residual_varianceEstimate residual variance
estimate_residual_variance_ssEstimate residual variance for summary statistics
est_V_unirootestimate prior variance
get_objectiveGet objective function from data and susie fit object.
get_objective_rssGet objective function from data and susie fit object.
get_objective_ssGet objective function from data and susie fit object.
is_symmetric_matrixcheck for symmetric matrix
loglikThe log likelihood function for SER model (based on summary...
muffled_corr'cor' function with specified warning muffled
muffled_cov2cor'cov2cor' function with specified warning muffled
predict.susiepredict future observations or extract coefficients from...
SER_posterior_e_loglik_rssposterior expected loglikelihood for a single effect...
set_R_attributessets the attributes for the R matrix
set_X_attributessets three attributes for matrix X
single_effect_regressionBayesian single-effect linear regression of Y on X
single_effect_regression_rssBayesian single-effect linear regression using z scores.
single_effect_regression_ssBayesian single-effect linear regression of y on X.
summary.susiesummarize susie fit
susieSUm of Single Effects (SuSiE) Regression
susie_autoAn attempt to automate reliable running of susie even on hard...
susie_bhatSummary statistics version of SuSiE on betahat, the...
susie_get_csExtract credible sets from SuSiE fit
susie_get_lfsrLocal false sign rate (lfsr) for susie credible sets
susie_get_objectiveGet evidence lower bound (ELBO) from fitted SuSiE model
susie_get_pipCompute posterior inclusion probability (PIP) for all...
susie_get_posterior_meanGet posterior mean for coefficients from fitted SuSiE model
susie_get_posterior_sdGet posterior standard deviation for coefficients from fitted...
susie_get_prior_varianceGet updated prior variance
susie_get_residual_varianceGet updated residual variance
susie_init_coefinitialize a susie object using regression coefficients
susie_plotPlot per variable summary in SuSiE CSs
susie_plot_changepointPlot changepoint data and susie fit using ggplot2
susie_plot_iterationDiagnostic plot for SuSiE iterations
susie_rssBayesian sum of single-effect (susie) linear regression using...
susie_slimSlim the result of fitted SuSiE model
susie_ssBayesian sum of single-effect (susie) linear regression using...
susie_trendfilterApplies susie to perform trend filtering (especially...
update_each_effectupdate each effect once
update_each_effect_rssupdate each effect once
update_each_effect_ssupdate each effect once
stephenslab/susieR documentation built on Aug. 12, 2019, 2:17 p.m.