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:

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]