EstimateRearrangementScenarios {SynExtend} | R Documentation

## Estimate Genome Rearrangement Events with Double Cut and Join Operations

### Description

Take in a Synteny object from FindSynteny and return predicted rearrangement events.

### Usage

    EstimateRearrangementScenarios(synt,
                                   num_runs = -1,
                                   verbose = TRUE,
                                   mean = FALSE,
                                   opp_value = 0,
                                   min_unique_length = 10,
                                   min_block_length = -1,
                                   actual = c(),
                                   test_run = 0)

### Arguments

`synt` | Synteny object obtained from running the FindSynteny object. Expected input is unichromosomal sequences, though multichromosomal sequences are supported.
`num_runs` | Numeric; Number of times to simulate scenarios. The default value of -1 (and all non-positive values) runs each analysis for 2b iterations, where b is the number of unique breakpoints.
`mean` | If TRUE, returns the mean number of inversions and transpositions found. If FALSE, returns the scenario corresponding to the minimum total number of operations across all runs. This parameter only affects the number of inversions and transpositions reported; the specific scenario returned is one of the runs that resulted in a minimum value.
`min_block_length` | Minimum size of syntenic blocks to use for analysis. The default value accepts all blocks. Set to a larger value to ignore sections of short mutations that could be the result of SNPs or other small-scale mutations.
`verbose` | Displays progress bars if verbose=TRUE.
`opp_value` | A parameter.
`min_unique_length` | A parameter.
`actual` | A parameter.
`test_run` | A parameter.

### Details

`EstimateRearrangementScenarios` is an implementation of the Double Cut and Join (DCJ) method for analyzing large scale mutation events. This implementation incentivizes minimum number of total events rather than total number of DCJs. Multiple scenarios are computed, and results of estimation are returned to the user.

### Value

An NxN matrix with the same shape as the input Synteny object.

The diagonal corresponds to total sequence length of the corresponding genome.

In the upper triangle, entry `[i,j]` corresponds to the percent hits between genome `i` and genome `j`. In the lower triangle, entry `[i,j]` contains a List object with 5 properties:

- `$Inversions` and `$Transpositions` contain the (mean/min) number of estimated inversions and transpositions (resp.) between genome `i` and genome `j`.

- `$pct_hits` contains percent hits between the genomes.

- `$Scenario` shows a rearrangement scenario resulting in a minimum number of events between the genomes, using permutation matrix notation. Each line shows the operation performed, the permutation vector corresponding to the current state relative to genome 1, and the number of blocks modified by the previous step.

- `$Key` displays a key for converting from permutation matrix to genomes. This matrix contains the start index for each block on each genome, the length of the block, the relative direction of the block on genome 2 compared to genome 1, and the permutation number for that block.

### Note

A note.

### Author(s)

Aidan Lakshman (ahl27@pitt.edu)

### References

Friedberg, R., Darling, A. E., & Yancopoulos, S. (2008). Genome rearrangement by the double cut and join operation. Bioinformatics, 385-416.

### See Also

`FindSynteny`

### Examples

    db <- system.file("extdata", "Influenza.sqlite", package="DECIPHER")
    synteny <- FindSynteny(db)
    synteny

    rearrs <- EstimateRearrangementScenarios(synteny)

    rearrs          # view whole object
    rearrs[[2,1]]   # view details on Genomes 1 and 2

[Package SynExtend version 1.6.0 Index]