select_segreg: Show markers with/without segregation distortion

In onemap: Construction of Genetic Maps in Experimental Crosses

Show markers with/without segregation distortion

Description

A function to shows which marker have segregation distortion if Bonferroni's correction is applied for the Chi-square tests of mendelian segregation.

Usage

select_segreg(x, distorted = FALSE, numbers = FALSE, threshold = NULL)

Arguments

x	an object of class onemap_segreg_test
distorted	a TRUE/FALSE variable to show distorted or non-distorted markers
numbers	a TRUE/FALSE variable to show the numbers or the names of the markers
threshold	a number between 0 and 1 to specify the threshold (alpha) to be considered in the test. If NULL, it uses the threshold alpha = 0.05. Bonferroni correction is applied for multiple test correction.

Value

a vector with marker names or numbers, according to the option for "distorted" and "numbers"

Examples

 # Loads a fake backcross dataset installed with onemap
 data(onemap_example_out)
 # Performs the chi-square test for all markers
 Chi <- test_segregation(onemap_example_out)
 # To show non-distorted markers
 select_segreg(Chi)
 # To show markers with segregation distortion
 select_segreg(Chi, distorted=TRUE)
 # To show the numbers of the markers with segregation distortion
 select_segreg(Chi, distorted=TRUE, numbers=TRUE)

onemap documentation built on Nov. 26, 2022, 9:05 a.m.