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Merged
pribiller merged 1 commit into from
Sep 2, 2026
Merged

The inversion clown… find it in your data. #63

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6 changes: 4 additions & 2 deletions R/StructuralVariants.R
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Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,12 @@
#' @aliases exampleDoubleInversion1 exampleDoubleInversion2
#' @aliases exampleDoubleInversion3 exampleDoubleInversion4
#' @aliases exampleTwinInversions exampleNotTwinInversions
#' @aliases exampleInversionGarg2019 exampleInversionBader2001
#' @aliases exampleInversionHP1999fig4a exampleInversionHP1999fig4b
#' @aliases exampleInversionGarg2019 exampleInversionBader2001
#' @aliases exampleInversionHP1999fig4a exampleInversionHP1999fig4b
#' @aliases exampleInversionBergeron2005a exampleInversionBergeron2005b
#' @aliases exampleTranslocation exampleTranslocation2
#' @aliases exampleInsertion exampleDeletion
#' @aliases exampleClownInversion
#'
#' @family Structural variants
#'
Expand All @@ -37,6 +38,7 @@
#' exampleInversion5uncollapsed
#' exampleNestedInversions
#' exampleDoubleInversion1
#' exampleClownInversion
#' exampleTwinInversions
#' exampleInversionGarg2019
#' exampleInversionBader2001
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13 changes: 12 additions & 1 deletion data-raw/StructuralVariants.R
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Expand Up @@ -95,6 +95,16 @@ exampleDoubleInversion4 <- GBreaks(exampleDoubleInversion4)
seqlengths(exampleDoubleInversion4) <- seqlengths(exampleDoubleInversion4$query) <- 600
isSorted(exampleDoubleInversion4)

# Clown inversion based on exampleDoubleInversion4
# ABC/cba -> ABC/cAB -> ABC/aCB => 1-, 3+, 2+

exampleClownInversion <- GRanges(c("chrA:100-190", "chrA:200-290", "chrA:300-340", "chrA:341-370","chrA:371-390", "chrA:400-490", "chrA:500-590"))
strand(exampleClownInversion) <- c( "-", "-", "+", "-", "+", "+", "-" )
exampleClownInversion$query <- GRanges(c("chrB:500-590", "chrB:200-290", "chrB:400-440", "chrB:441-470","chrB:471-490", "chrB:300-390", "chrB:100-190"))
exampleClownInversion <- GBreaks(exampleClownInversion)
seqlengths(exampleClownInversion) <- seqlengths(exampleClownInversion$query) <- 600
isSorted(exampleClownInversion)

# Nested inversions
# ABCDE -> AdcbE -> AdCbE

Expand Down Expand Up @@ -126,7 +136,7 @@ isSorted(exampleNotTwinInversions)

# Example used in the paper from Garg et al. (2019).
# {-2,5,4,-1,3,6,9,-7,-8}
# Reversal distance = 5 reversals.
# Reversal distance = 5 reversals.
# Details for Reversal distance (d) computation: 10 breakpoints (b); 5 cycles(c); 0 hurdles(h): d = b-c+h (+1 if fortress).
exampleInversionGarg2019 <- GRanges(c("chrA:100-190", "chrA:200-290", "chrA:300-390", "chrA:400-490", "chrA:500-590", "chrA:600-690", "chrA:700-790", "chrA:800-890", "chrA:900-990"))
strand(exampleInversionGarg2019) <- c( "-", "+", "+", "-", "+", "+", "+", "-", "-")
Expand Down Expand Up @@ -255,6 +265,7 @@ usethis::use_data(
exampleDoubleInversion2,
exampleDoubleInversion3,
exampleDoubleInversion4,
exampleClownInversion,
exampleNestedInversions,
exampleTwinInversions,
exampleNotTwinInversions,
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2 changes: 2 additions & 0 deletions man/StructuralVariants.Rd
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8 changes: 8 additions & 0 deletions vignettes/StructuralVariants.Rmd
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Expand Up @@ -202,6 +202,14 @@ exampleInversionBergeron2005a |> plotApairOfChrs(main = "Mathematics of Evolutio
exampleInversionBergeron2005b |> plotApairOfChrs(main = "Mathematics of Evolution and Phylogeny (2005) - Figure 10.6")
```

### The inversion clown.

Find it in your alignments!

```{r inversionClown}
exampleClownInversion |> makeOxfordPlots(col = "strand") + ggplot2::theme_bw()
```

## Translocations

If a region has moved, but is not an inversion, then it is a translocation.
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