Fix Rd cross-reference WARNING on macOS/Windows

Replace \link[echolocatoR] and \link[TFBSTools] with \code{} refs —
these packages are not available on all CI platforms, causing
"Unknown package" / "Missing link" warnings that are fatal with
error_on="warning".

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: bschilder

R/CS_bin_plot.R

@@ -2,7 +2,7 @@
 #' 
 #' Plot Credible Set bins counts for multiple fine-mapping method results.
 #' @param merged_DT Merged fine-mapping results data from
-#'  \link[echolocatoR]{finemap_loci}.
+#'  \code{echolocatoR::finemap_loci}.
 #' @param show_plot Show plot. 
 #'
 #' @family summarise

R/MOTIFBREAKR.R

@@ -31,7 +31,7 @@
 #' Otherwise, import the existing results and skip the analyses
 #'  (default: \code{FALSE}).
 #' @param pwmList An object of class
-#'  \link[TFBSTools]{MotifList} containing position weight matrices.
+#'  \code{TFBSTools::MotifList} containing position weight matrices.
 #'  If \code{NULL}, defaults to \code{MotifDb::MotifDb}.
 #' @param threshold A numeric value used as a threshold for filtering results.
 #' @param show.neutral Logical. Include neutral effects in results.

R/NOTT2019_epigenomic_histograms.R

@@ -2,7 +2,7 @@
 #'
 #' Brain cell-specific epigenomic data from Nott et al. (2019).
 #' 
-#' @param dat Fine-mapping results data from \link[echolocatoR]{finemap_loci}.
+#' @param dat Fine-mapping results data from \code{echolocatoR::finemap_loci}.
 #' @param locus_dir Locus-specific directory.
 #' @param show_plot Show plot.
 #' @param save_plot Whether to save the plot. 

R/annotate_missense.R

@@ -2,7 +2,7 @@
 #'
 #' Annotate any missense variants with \link[biomaRt]{getBM}.
 #' @param merged_DT Merged fine-mapping results data from
-#'  \link[echolocatoR]{finemap_loci}.
+#'  \code{echolocatoR::finemap_loci}.
 #' @param snp_filter Row-wise filter to apply to \code{merged_DT} filter 
 #' (provided as a string). 
 #' 

R/plot_dataset_overlap.R

@@ -3,7 +3,7 @@
 #' Cross-tabulate SNP overlap (after applying filter)
 #' between each pair of studies.
 #' @param merged_DT Merged fine-mapping results data from
-#'  \link[echolocatoR]{finemap_loci}.
+#'  \code{echolocatoR::finemap_loci}.
 #' @param triangle Plot correlation matrix as a square or a triangle.
 #' @param filename Path to save file to as PNG.
 #' @param formula_str Formula passed to \link[stats]{xtabs}.

R/super_summary_plot.R

@@ -2,7 +2,7 @@
 #'
 #' @family summarise
 #' @param merged_DT Merged fine-mapping results data from
-#'  \link[echolocatoR]{finemap_loci}.
+#'  \code{echolocatoR::finemap_loci}.
 #' @param snp_filter Filter to use apply to SNPs before plotting.
 #' @param coloc_results Colocalization results from 
 #' \href{https://github.com/RajLabMSSM/catalogueR}{catalogueR}.