Fix Rd \usage WARNING and NSE global variable NOTEs

- Remove stray @param A/B from test_enrichment (not in function signature)
- Add Cell_type/Assay bindings to suppress NSE global variable NOTEs
- Fix NOTT2019_get_interactions: use seqnames as chrom_col in dt_to_granges

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

Author: bschilder

R/XGR_plot_enrichment.R

@@ -20,7 +20,7 @@ XGR_plot_enrichment <- function(enrich_res,
                                 show_plot = TRUE) {
 
     requireNamespace("ggplot2")
-    fc <- adjp <- assay <- NULL;
+    fc <- adjp <- assay <- Cell_type <- Assay <- NULL;
     enrich_res <- dplyr::arrange(enrich_res, dplyr::desc(fc))
     enrich_res$source <- factor(enrich_res$source,
         unique(enrich_res$source),

R/initialize_plac_seq_plot.R

@@ -6,7 +6,8 @@ initialize_plac_seq_plot <- function(interact.DT,
                                      strip.text.y.angle,
                                      verbose = TRUE){
     requireNamespace("ggplot2")
-    messager("Initializing PLAC-seq plot.",v=verbose) 
+    Cell_type <- NULL;
+    messager("Initializing PLAC-seq plot.",v=verbose)
     if (highlight_plac) {
         ##### Method 1 #####
         ### Apply alpha based on consensus SNP overlap

R/test_enrichment.R

@@ -23,12 +23,6 @@
 #' @param verbose Print messages.
 #' @param save_path Path to save results to as an \emph{RDS} file.
 #' Set to \code{NULL} to skip this step.
-#' @param A A region set in any of the accepted formats by
-#' \code{\link[regioneR]{toGRanges}}
-#' (\link[GenomicRanges]{GRanges}, \code{data.frame}, etc.).
-#' @param B A region set in any of the accepted formats by
-#' \code{\link[regioneR]{toGRanges}}
-#' (\link[GenomicRanges]{GRanges}, \code{data.frame}, etc.).
 #' @inheritDotParams regioneR::overlapPermTest
 #' @inheritParams regioneR::permTest 
 #' @source \href{https://www.bioconductor.org/packages/devel/bioc/vignettes/regioneR/inst/doc/regioneR.html}{