fgt_rrate_dpr: Four Gametes Test, R^2 and LD' Calculation

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/fgt_rrate_dpr.R

Description

This helper function calculates three summary statistics of the regression model. Here, the four gametes test, R^2, and LD' are calculated for each pair of sites and returned to its calling function (summary_statistics)

Usage

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fgt_rrate_dpr(x, y, data1, data2)

Arguments

x

Site 1

y

Site 2

data1

Data set to calculate the first two summary statistics

data2

Data set to calculate the four gametes test

Value

A vector is returned containing three values for:

fgt

An indicator value whether the four gametes test indicates a recombination event

R^2

for the pair of sites x and y using diseq, genotype

LD'

for the pair of sites x and y using diseq, genotype

Author(s)

Philipp Hermann [email protected], Andreas Futschik

References

Gregory Warnes, with contributions from Gregor Gorjanc, Friedrich Leisch and Michael Man. (2013). genetics: Population Genetics. R package version 1.3.8.1.

See Also

LDJump, vcfR_to_fasta, summary_statistics, get_smuce, diseq, genotype

Examples

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##### Do not run these examples                                          #####
##### In summary_statistics.R the function is called as follows          #####
##### helper = mapply(fgt_rrate_dpr, x = indices[,1], y = indices[,2],   #####
#####                 MoreArgs = list(data1 = g2dftemp, data2 = samp))   #####

PhHermann/LDJump documentation built on Oct. 18, 2018, 11:06 a.m.