testDistortion: Test for distortion using IBD genotype probabilities

In mpMap2: Genetic Analysis of Multi-Parent Recombinant Inbred Lines

Description

Test for distortion using IBD genotype probabilities

Usage

testDistortion(object)

Arguments

object

An object of class mpcrossMapped which contains imputed IBD genotype data

Details

In real experiments, genetic inheritance may not follow the expected model. This function tests for deviations from expected inheritance by using the genetic composition of the population at individual positions, as measured by the IBD genotype probabilities.

At a particular point, the mean for each founder allele of the IBD genotype probabilities for each founder allele are summed across the population. The average is taken, and this is then compared with the proportion expected to be inherited from that founder, under standard models of genetic inheritance.

The result is a matrix containing p-values, test-statistic values, and the L1 and L2 distances between the observed genetic proportions, and the expected genetic proportions.

Value

A data.frame containing p-values and test-statistic values for each position at which there is IBD genotype probability data.

mpMap2 documentation built on Sept. 13, 2020, 5:17 p.m.