summarizeRearrs: Summarize Rearrangements
In dorolin/rearrvisr: Detect, Classify, and Visualize Genome Rearrangements

Description Usage Arguments Details Value See Also Examples

For each focal genome segment, summarize the number and type of rearrangement events and the number of breakpoints

1 2	summarizeRearrs(SYNT, focalgenome, compgenome, ordfocal, remWgt = 0.05, remThld = 0)

`SYNT`	A list of matrices that store data on different classes of rearrangements and additional information. `SYNT` must have been generated with the `computeRearrs` function (optionally filtered with the `filterRearrs` function).
`focalgenome`	Data frame representing the focal genome, containing the mandatory columns `$marker`, `$scaff`, `$start`, `$end`, and `$strand`, and optional further columns. Markers need to be ordered by their map position.
`compgenome`	Data frame representing the compared genome (e.g., an ancestral genome reconstruction, or an extant genome), with the first three columns `$marker`, `$orientation`, and `$car`, followed by columns alternating node type and node element. Markers need to be ordered by their node elements. `compgenome` must be the same data frame that was used to generate the list `SYNT` with the `computeRearrs` function.
`ordfocal`	Character vector with the IDs of the focal genome segments that will be summarized. Have to match (a subset of) IDs in `focalgenome$scaff`.
`remWgt`	A numeric value between `0` (inclusive) and `0.5` (exclusive). Needs to match the value for `remWgt` used in the `computeRearrs` function.
`remThld`	A numeric value between `0` (inclusive) and `0.5` (exclusive). Controls whether breakpoints for components of rearrangements that are less parsimonious to have changed position relative to the alternative components will be output. To output all breakpoints, `remThld` needs to be smaller than `remWgt` used in the `computeRearrs` function.

Only rearrangements that have components tagged with values larger than remWgt will be counted. For proper functioning, remWgt should correspond to the value that has been used to generate SYNT. The number of nonsyntenic moves is computed as the maximum of class I and class II nonsyntenic moves per focal genome segment.

The number of breakpoints is computed based on the getBreakpoints function. To include the breakpoint of origin for nonsyntenic and syntenic moves in the estimate, remThld needs to be set to zero (which is the default). Note that this may nevertheless underestimate the number of breakpoints as the location of origin is not determined for all rearrangements. When the input is a filtered version of SYNT (i.e., filtered with the filterRearrs function), the number of breakpoints may be overestimated. This can be prevented by increasing the value of remThld to match the value of remWgt. However, this may then underestimate the number of breakpoints as some breakpoints of origin will not be counted. Breakpoints that fall on identical positions are only counted once.

A matrix with the number of identified nonsyntenic moves, syntenic moves, inversions, and breakpoints in columns, for the set of focal genome segments in ordfocal in rows.

computeRearrs, filterRearrs, getBreakpoints.

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SYNT <- computeRearrs(TOY24_focalgenome, TOY24_compgenome, doubled = TRUE)

summarizeRearrs(SYNT, TOY24_focalgenome, TOY24_compgenome, c("1","2","3"))