new feature: cytobands coordinates

R/cool_overlaps.R

@@ -113,11 +113,13 @@ cool_overlaps <- function(
 
     # When the same columns are provided they will become .x and .y
     if(start1 == start2) {
+        original_start1 <- start1
         start1 <- paste0(start1, ".x")
         start2 <- paste0(start2, ".y")
 
     }
     if(end1 == end2) {
+        original_end1 <- end1
         end1 <- paste0(end1, ".x")
         end2 <- paste0(end2, ".y")
 
@@ -193,6 +195,20 @@ cool_overlaps <- function(
                 overlap
             )
         )
+        if(original_start1 %in% colnames(no_annotation)){
+            colnames(no_annotation) = gsub(
+                original_start1,
+                start1,
+                colnames(no_annotation)
+            )
+        }
+        if(original_end1 %in% colnames(no_annotation)){
+            colnames(no_annotation) = gsub(
+                original_end1,
+                end1,
+                colnames(no_annotation)
+            )
+        }
         overlap <- bind_rows(
             overlap,
             no_annotation

R/data.R

@@ -980,3 +980,33 @@
 #'   \item{Description}{NA.}
 #' }
 "protein_domains"
+
+#' Cytobands coordinates (grch37)
+#'
+#' A data frame in bed format with coordinates of cytobands relative to grch37.
+#'
+#' @format ## `cytobands_grch37`
+#' A data frame with 862 rows and 5 columns
+#' \describe{
+#'   \item{cb.chromosome}{Chromosome of the cytoband.}
+#'   \item{cb.start}{Start position of the cytoband.}
+#'   \item{cb.end}{End position of the cytoband.}
+#'   \item{cb.name}{Cytoband name.}
+#'   \item{label}{Cytoband label.}
+#' }
+"cytobands_grch37"
+
+#' Cytobands coordinates (hg38)
+#'
+#' A data frame in bed format with coordinates of cytobands relative to hg38.
+#'
+#' @format ## `cytobands_hg38`
+#' A data frame with 862 rows and 5 columns
+#' \describe{
+#'   \item{cb.chromosome}{Chromosome of the cytoband.}
+#'   \item{cb.start}{Start position of the cytoband.}
+#'   \item{cb.end}{End position of the cytoband.}
+#'   \item{cb.name}{Cytoband name.}
+#'   \item{label}{Cytoband label.}
+#' }
+"cytobands_hg38"

data-raw/DATASET.R

@@ -509,3 +509,20 @@ protein_domains <- system.file(
     ) %>%
     read_tsv()
 usethis::use_data(protein_domains, overwrite = TRUE)
+
+# Cytobands
+cytobands_grch37 <- system.file(
+        "extdata",
+        "cytobands_grch37.tsv",
+        package = "GAMBLR.data"
+    ) %>%
+    read_tsv()
+usethis::use_data(cytobands_grch37, overwrite = TRUE)
+
+cytobands_hg38 <- system.file(
+        "extdata",
+        "cytobands_hg38.tsv",
+        package = "GAMBLR.data"
+    ) %>%
+    read_tsv()
+usethis::use_data(cytobands_hg38, overwrite = TRUE)