diff --git a/R/regularized_regression.R b/R/regularized_regression.R index 2557115e..5e5adf2b 100644 --- a/R/regularized_regression.R +++ b/R/regularized_regression.R @@ -375,7 +375,7 @@ susie_weights <- function(X = NULL, y = NULL, susie_fit = NULL, ...) { susie_ash_weights <- function(X = NULL, y = NULL, susie_ash_fit = NULL, ...) { if (is.null(susie_ash_fit)) { # get susie_ash_fit object - susie_ash_fit <- susie_wrapper(X, y, unmappable_effects = "ash", standardize = FALSE, intercept = FALSE, ...) + susie_ash_fit <- susie_wrapper(X, y, unmappable_effects = "ash", convergence_method = "pip", ...) } if (!is.null(X)) { if (length(susie_ash_fit$pip) != ncol(X)) { @@ -385,7 +385,7 @@ susie_ash_weights <- function(X = NULL, y = NULL, susie_ash_fit = NULL, ...) { )) } } - if ("alpha" %in% names(susie_ash_fit) && "mu" %in% names(susie_ash_fit) && "X_column_scale_factors" %in% names(susie_ash_fit)) { + if ("alpha" %in% names(susie_ash_fit) && "mu" %in% names(susie_ash_fit) && "theta" %in% names(susie_ash_fit) && "X_column_scale_factors" %in% names(susie_ash_fit)) { # This is designed to cope with output from pecotmr::susie_post_processor() # We set intercept to 0 and later trim it off anyways susie_ash_fit$intercept <- 0 @@ -400,7 +400,7 @@ susie_ash_weights <- function(X = NULL, y = NULL, susie_ash_fit = NULL, ...) { susie_inf_weights <- function(X = NULL, y = NULL, susie_inf_fit = NULL, ...) { if (is.null(susie_inf_fit)) { # get susie_inf_fit object - susie_inf_fit <- susie_wrapper(X, y, unmappable_effects = "inf", standardize = FALSE, intercept = FALSE, ...) + susie_inf_fit <- susie_wrapper(X, y, unmappable_effects = "inf", convergence_method = "pip", ...) } if (!is.null(X)) { if (length(susie_inf_fit$pip) != ncol(X)) { @@ -410,7 +410,7 @@ susie_inf_weights <- function(X = NULL, y = NULL, susie_inf_fit = NULL, ...) { )) } } - if ("alpha" %in% names(susie_inf_fit) && "mu" %in% names(susie_inf_fit) && "X_column_scale_factors" %in% names(susie_inf_fit)) { + if ("alpha" %in% names(susie_inf_fit) && "mu" %in% names(susie_inf_fit) && "theta" %in% names(susie_inf_fit) && "X_column_scale_factors" %in% names(susie_inf_fit)) { # This is designed to cope with output from pecotmr::susie_post_processor() # We set intercept to 0 and later trim it off anyways susie_inf_fit$intercept <- 0