TOY24_compgenome: 'compgenome' example for 24 markers, created for illustrative...
In dorolin/rearrvisr: Detect, Classify, and Visualize Genome Rearrangements

Description Usage Format See Also Examples

A data set illustrating a compared (ancestral or extant) genome representation with 24 markers on four Contiguous Ancestral Regions (CARs), where each CAR is represented by a PQ-tree.

1	TOY24_compgenome

A data frame with markers in rows and nine columns that specify the structure of a compared genome representation:

`$marker`	unique ortholog ID of marker
`$orientation`	reading direction of marker
`$car`	CAR where marker is located
`$type1`	node type at highest level of PQ-tree
`$elem1`	node element at highest level of PQ-tree
`$type2`	node type at second level of PQ-tree
`$elem2`	node element at second level of PQ-tree
`$type3`	node type at third level of PQ-tree
`$elem3`	node element at third level of PQ-tree

computeRearrs, TOY24_focalgenome

## Not run: 

## recreate the data set
TOY24_rawtree <- matrix(
  c(">TOY",
    "#CAR1",
    "_Q 1 2 3 4 5 -6 7 8 Q_",
    "#CAR2",
    "_Q 9 _Q 10 Q_ _Q 11 12 13 Q_ Q_",
    "#CAR3",
    "_Q 14 Q_",
    "#CAR4",
    "_Q _P 15 16 17 18 P_ _Q _Q -19 20 21 Q_ _Q -22 -23 24 Q_ Q_ Q_"),
  nrow = 9)
TOY24_compgenome <- convertPQtree(TOY24_rawtree)

## End(Not run)