simple fix - removing colocboost::

DESCRIPTION

@@ -25,6 +25,7 @@ Imports:
     S4Vectors,
     SummarizedExperiment,
     coloc,
+    colocboost,
     dplyr,
     magrittr,
     matrixStats,
@@ -47,7 +48,6 @@ Suggests:
     bigsnpr,
     bigstatsr,
     coda,
-    colocboost,
     flashier,
     fsusieR,
     GBJ,

NAMESPACE

@@ -286,6 +286,7 @@ importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,rowRanges)
 importFrom(coloc,coloc.bf_bf)
+importFrom(colocboost,colocboost)
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,any_of)

R/colocboost_pipeline.R

@@ -14,8 +14,9 @@ build_ld_args <- function(ld_list, subset = NULL) {
   if (is_geno) list(X_ref = ld_list) else list(LD = ld_list)
 }
 
-# Run colocboost with tryCatch and timing.
-# @noRd
+#' Run colocboost with tryCatch and timing.
+#' @importFrom colocboost colocboost
+#' @noRd
 .run_colocboost <- function(label, ...) {
   t1 <- Sys.time()
   res <- tryCatch(
@@ -32,7 +33,7 @@ build_ld_args <- function(ld_list, subset = NULL) {
   if (!requireNamespace("colocboost", quietly = TRUE)) {
     stop("The colocboost package is required for colocboost_analysis().")
   }
-  do.call(colocboost::colocboost, c(args, dots))
+  do.call(colocboost, c(args, dots))
 }
 
 #' Convert loaded regional data to ColocBoost inputs
@@ -94,7 +95,7 @@ region_data_to_colocboost_input <- function(region_data) {
 #' This wrapper keeps the direct \code{colocboost()} argument surface. All
 #' ColocBoost inputs and model parameters are supplied through \code{...}. When
 #' no QC options are requested, the call is passed directly to
-#' \code{colocboost::colocboost()}. When QC options are requested, the wrapper
+#' \code{colocboost()}. When QC options are requested, the wrapper
 #' inspects named \code{X}/\code{Y} and/or \code{sumstat}/\code{LD}/\code{X_ref}
 #' arguments in \code{...}, runs the relevant reusable QC step, and then calls
 #' ColocBoost on the cleaned inputs. If the required named inputs are not
@@ -103,7 +104,7 @@ region_data_to_colocboost_input <- function(region_data) {
 #'
 #' @details
 #' Use \code{colocboost_analysis()} the same way you would use
-#' \code{colocboost::colocboost()}: pass the native ColocBoost arguments by
+#' \code{colocboost()}: pass the native ColocBoost arguments by
 #' name, for example \code{X}, \code{Y}, \code{sumstat}, \code{LD},
 #' \code{X_ref}, \code{dict_YX}, \code{dict_sumstatLD},
 #' \code{outcome_names}, \code{focal_outcome_idx}, \code{effect_est},
@@ -123,13 +124,13 @@ region_data_to_colocboost_input <- function(region_data) {
 #' \code{impute = TRUE}.
 #'
 #' If no QC controls are supplied, this function is a thin direct call to
-#' \code{colocboost::colocboost(...)}.
+#' \code{colocboost(...)}.
 #' When QC removes outcomes, \code{outcome_names} and \code{focal_outcome_idx}
 #' are updated to match the post-QC outcome order. If the requested focal outcome
 #' is removed by QC, \code{focal_outcome_idx} is set to \code{NULL} with a
 #' warning.
 #'
-#' @param ... Arguments passed to \code{colocboost::colocboost()}, including
+#' @param ... Arguments passed to \code{colocboost()}, including
 #'   data inputs such as \code{X}, \code{Y}, \code{sumstat}, \code{LD},
 #'   \code{X_ref}, \code{dict_YX}, \code{dict_sumstatLD},
 #'   \code{outcome_names}, and all ColocBoost model/post-processing options.
@@ -148,12 +149,12 @@ region_data_to_colocboost_input <- function(region_data) {
 #'   parseable genomic variant IDs. It can be a .bim/.pvar/.pvar.zst file path,
 #'   a data.frame with variant metadata, or a \code{load_LD_matrix()} result.
 #'   This is a QC-only argument and is not passed to
-#'   \code{colocboost::colocboost()}.
+#'   \code{colocboost()}.
 #' @param variant_convention Allele order used by native ColocBoost-style
 #'   \code{sumstat$variant} and LD/X_ref names when deriving QC inputs:
 #'   \code{"A2_A1"} for pecotmr canonical \code{chr:pos:A2:A1}, or
 #'   \code{"A1_A2"} for \code{chr:pos:A1:A2}.
-#' @return The object returned by \code{colocboost::colocboost()}.
+#' @return The object returned by \code{colocboost()}.
 #' @examples
 #' \dontrun{
 #' # Direct ColocBoost call without QC.