Fix a bug of susie_weights_intermediate logic

cumc · Sep 15, 2024 · 1d2bb9d · 1d2bb9d
1 parent 904249b
commit 1d2bb9d
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/R/twas_weights.R b/R/twas_weights.R
@@ -445,6 +445,10 @@ twas_weights_pipeline <- function(X,
  # TWAS weights and predictions
  if (!is.null(susie_fit) && !is.null(weight_methods$susie_weights)) {
  weight_methods$susie_weights <- list(susie_fit = susie_fit)
+ res$susie_weights_intermediate <- susie_fit[c("mu", "lbf_variable", "X_column_scale_factors")]
+ if (!is.null(susie_fit$sets$cs)) {
+ res$susie_weights_intermediate$cs_variants <- lapply(susie_fit$sets$cs, function(L) colnames(X)[L])
+ }
  }
  res$twas_weights <- twas_weights(X, y, weight_methods = weight_methods)
  res$twas_predictions <- twas_predict(X, res$twas_weights)
@@ -481,10 +485,6 @@ twas_weights_pipeline <- function(X,
  num_threads = cv_threads,
  variants_to_keep = if (length(variants_for_cv) > 0) variants_for_cv else NULL
  )
- res$susie_weights_intermediate <- susie_fit[c("mu", "lbf_variable", "X_column_scale_factors")]
- if (!is.null(susie_fit$sets$cs)) {
- res$susie_weights_intermediate$cs_variants <- lapply(susie_fit$sets$cs, function(L) colnames(X)[L])
- }
  }
  res$total_time_elapsed <- proc.time() - st