From 85f877faaf0d07670cb49dee9c05741fe832ccba Mon Sep 17 00:00:00 2001 From: alexmccreight <57416850+alexmccreight@users.noreply.github.com> Date: Sat, 1 Nov 2025 13:59:19 -0500 Subject: [PATCH] ash residual variance update parameter --- R/sufficient_stats_methods.R | 2 +- R/susie.R | 3 ++- R/susie_constructors.R | 2 ++ 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/R/sufficient_stats_methods.R b/R/sufficient_stats_methods.R index b1b86092..922955c5 100644 --- a/R/sufficient_stats_methods.R +++ b/R/sufficient_stats_methods.R @@ -360,7 +360,7 @@ update_variance_components.ss <- function(data, params, model, ...) { intercept = FALSE, standardize = FALSE, sigma2 = mom_result$sigma2, - update.sigma2 = FALSE, + update.sigma2 = params$update_ash_sigma2, max.iter = 3000 ) diff --git a/R/susie.R b/R/susie.R index e30aecf9..e41bc199 100644 --- a/R/susie.R +++ b/R/susie.R @@ -279,6 +279,7 @@ susie <- function(X, y, L = min(10, ncol(X)), estimate_prior_variance = TRUE, estimate_prior_method = c("optim", "EM", "simple"), unmappable_effects = c("none", "inf", "ash"), + update_ash_sigma2 = FALSE, check_null_threshold = 0, prior_tol = 1e-9, residual_variance_upperbound = Inf, @@ -310,7 +311,7 @@ susie <- function(X, y, L = min(10, ncol(X)), prior_weights, null_weight, standardize, intercept, estimate_residual_variance, estimate_residual_method, estimate_prior_variance, estimate_prior_method, - unmappable_effects, check_null_threshold, prior_tol, + unmappable_effects, update_ash_sigma2, check_null_threshold, prior_tol, residual_variance_upperbound, model_init, coverage, min_abs_corr, compute_univariate_zscore, na.rm, max_iter, tol, convergence_method, verbose, track_fit, diff --git a/R/susie_constructors.R b/R/susie_constructors.R index 355caa13..80c9d8a4 100644 --- a/R/susie_constructors.R +++ b/R/susie_constructors.R @@ -24,6 +24,7 @@ individual_data_constructor <- function(X, y, L = min(10, ncol(X)), estimate_prior_variance = TRUE, estimate_prior_method = "optim", unmappable_effects = "none", + update_ash_sigma2 = FALSE, check_null_threshold = 0, prior_tol = 1e-9, residual_variance_upperbound = Inf, @@ -140,6 +141,7 @@ individual_data_constructor <- function(X, y, L = min(10, ncol(X)), estimate_prior_variance = estimate_prior_variance, estimate_prior_method = estimate_prior_method, unmappable_effects = unmappable_effects, + update_ash_sigma2 = update_ash_sigma2, check_null_threshold = check_null_threshold, prior_tol = prior_tol, residual_variance_upperbound = residual_variance_upperbound,