Update example in inversionDistance function

R/inversionDistance.R

@@ -22,13 +22,13 @@
 #' @return An integer: the minimal number of inversions needed to sort the permutation.
 #'
 #' @examples
-#' \dontrun{
 #' # Example using a permutation vector directly
 #' # Suppose we want to sort the permutation p = c(1, 3, -2, 4)
 #' inversionDistance(c(1, 3, -2, 4))
 #'
-#' # Example using a GBreaks object
-#' inversionDistance(exampleInversion2)}
+#' # Example using a GBreaks object.
+#' # This example is based on Figure 4(a) from Hannehalli and Pevzner (1999). The inversion distance is 8.
+#' inversionDistance(exampleInversionHP1999fig4a)
 #'
 #' @seealso \code{\link{permutationVector}} for generating the permutation vector.
 #'

data-raw/StructuralVariants.R

@@ -45,15 +45,6 @@ exampleInversion                          <- GBreaks(exampleInversion)
 seqlengths(exampleInversion)              <- seqlengths(exampleInversion$query) <- 600
 isSorted(exampleInversion)
 
-# Inversions 2
-
-exampleInversion2                          <- GRanges(c("chrA:100-190", "chrA:200-290", "chrA:300-390", "chrA:400-490", "chrA:500-590", "chrA:600-690"))
-strand(exampleInversion2)                  <- c(              "+",            "-",            "-",            "-",            "+",            "+"      )
-exampleInversion2$query                    <- GRanges(c("chrA:100-190", "chrA:300-390", "chrA:200-290", "chrA:400-490", "chrA:600-690", "chrA:500-590"))
-exampleInversion2                          <- GBreaks(exampleInversion2)
-seqlengths(exampleInversion2)              <- seqlengths(exampleInversion2$query) <- 700
-isSorted(exampleInversion2)
-
 # Inversion in a 5-bloc context with non-collapsed regions
 # This is an intermediary step towards `exampleDoubleInversion1`
 
@@ -259,7 +250,6 @@ usethis::use_data(
   exampleColinear3,
   exampleColinear5,
   exampleInversion,
-  exampleInversion2,
   exampleInversion5uncollapsed,
   exampleDoubleInversion1,
   exampleDoubleInversion2,