Merge pull request #33 from alexmccreight/master

ash residual variance update parameter

Author: alexmccreight

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
     )
 

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,

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,