FTTrecord: A Reference Class for storing and manipulating the results...

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

Description

A Reference Class for storing and manipulating the results and data from a four taxon test.

Fields

P1

Character The population which forms the P1 taxon in the four taxon test.

P2

Character The population which forms the P2 taxon in the four taxon test.

P3

Character The population which forms the P3 taxon in the four taxon test.

A

Character The population which forms the ancestral/outgroup taxon in the four taxon test.

numBlocks

integer The number of blocks the DNA sequence alignment was split into in order to perform the test.

blockLength

integer The number of base pairs to each block the DNA sequence alignment was split into to perform the test.

ABBA

numeric The global sum of ABBA sites. Given by (1 - Pr_1) * Pr_2 * Pr_3 * (1 - Pr_4). Where Pr_i is the frequency of the derived allele in the i'th population.

ABBA

numeric The global sum of BABA sites. Given by Pr_1 * (1 - Pr_2) * Pr_3 * (1 - Pr_4). Where Pr_i is the frequency of the derived allele in the i'th population.

ABBAcount

integer The number of sites for which ABBA was greater than BABA.

BABAcount

integer The number of sites for which BABA was greater than ABBA.

globalX2

numeric A chi squared value computed during the four taxon test. Used to assess whether ABBAcount and BABAcount are significantly different, based on the binomial distribution.

X2_P

numeric A p-value computer by the Fisher combined probability test based on globalX2. Indicates whether ABBAcount and BABAcount differ significantly.

D_jEstimate

numeric Patterson's D estimate based on jackknifeing the blocks of data.

Fd_1DD4_jEstimate

numeric A jackknifed estimate of Fd for complete introgression between populations 2 and 3.

Fd_D2D4_jEstimate

numeric A jackknifed estimate of Fd for complete introgression between populations 1 and 3.

D_jVariance

numeric Variance of Pattersons D estimates from jackknife.

Fd_1DD4_jVariance

numeric Variance of Fd estimates from jackknife. Where Fd is for total introgression between Populations 2 and 3.

Fd_D2D4_jVariance

numeric Variance of Fd estimates from jackknife. Where Fd is for total introgression between Populations 1 and 3.

D_jSD

numeric Standard deviation of Patterson's D estimates from jackknife.

Fd_1DD4_jSD

numeric Standard deviation of Fd estimates from jackknife. Where Fd is for total introgression between Populations 2 and 3.

Fd_D2D4_jSD

numeric Standard deviation of Fd estimates from jackknife. Where Fd is for total introgression between Populations 1 and 3.

D_jZ

numeric The Z score of Patterson's D, computed from the jackknife data.

Fd_1DD4_jZ

numeric The Z score of Fd, computed from the jackknife data. Where Fd is calculated for complete introgression between populations 2 and 3.

Fd_D2D4_jZ

numeric The Z score of Fd, computed from the jackknife data. Where Fd is calculated for complete introgression between populations 1 and 3.

tableFile

character A character string indicating the temporary file used to store the dataframe accessed with the table field.

table

function An accessor function used to access a table of results stored in a temporary file on disk. The location of this file is indicated by the tableFile field.

Methods

blankTable()

Method clears the table.

getPops()

Gets the population names from the result.

getTable(includeGlobal, neat)

Gets the results table for the blocks used to analyze the data.

globallySignificant()

Returns true if the test is significant according to the binomial.

initialize(p1, p2, p3, a, HCDir)

Initialize the result object.

noTestPerformed()

Returns true if a test has not been performed yet.

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