BlockDatingSettings: A reference class storing the settings for recombination...

In Ward9250/HybridCheck: Detection and dating of Recombinant Regions in DNA sequence data

Description

A reference class storing the settings for recombination block dating.

Fields

MutationRate

Numeric vector of length one. Stores the mutation rate to be used when dating blocks.

PValue

Numeric vector of length one. Stores the critical alpha value for testing the signifcance of recombination regions.

BonfCorrection

Logical vector of length one, stores the option of whether the critical value stored in PValue will be corrected.

DateAnyway

Logical vector of length one, sotres the option of whether blocks will be dated despite failing the critical alpha.

MutationCorrection

Character vector of length 1, can be any of the model supported by the ape package. Default is "JC69".

Methods

setBonferonni(newBonf)

Set whether the critical value should be subject to bonferroni correction during block significance testing.

setDateAnyway(newValue)

Set whether blocks should be kept and dated even if they fail the significance test.

setMutationCorrection(model)

Set the model of sequence evolution to correct the distances/number of mutations used in block dating algorithm.

setMutationRate(newRate)

Sets a new mutation rate for the settings.

setPValue(newValue)

Set a new critical value for significance testing of recombinant blocks.

Ward9250/HybridCheck documentation built on Jan. 30, 2022, 11:01 a.m.